[{"doi":"10.1063/5.0304731","acknowledgement":"The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","quality_controlled":"1","volume":164,"status":"public","year":"2026","_id":"21408","date_published":"2026-02-28T00:00:00Z","citation":{"short":"M. Hübl, C.P. Goodrich, Journal of Chemical Physics 164 (2026).","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.” Journal of Chemical Physics. AIP Publishing, 2026. https://doi.org/10.1063/5.0304731.","ieee":"M. Hübl and C. P. Goodrich, “Simultaneous optimization of assembly time and yield in programmable self-assembly,” Journal of Chemical Physics, vol. 164, no. 8. AIP Publishing, 2026.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly Time and Yield in Programmable Self-Assembly.” Journal of Chemical Physics, vol. 164, no. 8, 084904, AIP Publishing, 2026, doi:10.1063/5.0304731.","ama":"Hübl M, Goodrich CP. Simultaneous optimization of assembly time and yield in programmable self-assembly. Journal of Chemical Physics. 2026;164(8). doi:10.1063/5.0304731","apa":"Hübl, M., & Goodrich, C. P. (2026). Simultaneous optimization of assembly time and yield in programmable self-assembly. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0304731"},"intvolume":" 164","publisher":"AIP Publishing","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"abstract":[{"lang":"eng","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."}],"corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","language":[{"iso":"eng"}],"article_number":"084904","oa":1,"scopus_import":"1","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"project":[{"grant_number":"FTI23-G-011","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"article_processing_charge":"Yes (via OA deal)","ddc":["540"],"month":"02","issue":"8","file_date_updated":"2026-03-09T10:38:55Z","date_updated":"2026-03-09T10:40:41Z","fulldoi":"https://doi.org/10.1063/5.0304731","OA_place":"publisher","publication":"Journal of Chemical Physics","date_created":"2026-03-08T23:01:45Z","title":"Simultaneous optimization of assembly time and yield in programmable self-assembly","has_accepted_license":"1","article_type":"original","file":[{"file_size":6903766,"file_name":"2026_JourChemPhysics_Huebl.pdf","date_updated":"2026-03-09T10:38:55Z","relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"21415","content_type":"application/pdf","checksum":"9bdb8870930e83edb973408da3038559","date_created":"2026-03-09T10:38:55Z"}],"OA_type":"hybrid","external_id":{"arxiv":["2510.07876"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","arxiv":1,"author":[{"full_name":"Hübl, Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl","first_name":"Maximilian"},{"last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"day":"28"},{"article_type":"original","file":[{"creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","file_size":2680924,"date_updated":"2026-03-23T15:53:29Z","file_name":"2026_PhysicalReviewResearch_Huebl.pdf","date_created":"2026-03-23T15:53:29Z","checksum":"6d8a68e4a19f8dad5abdf75f72316f3d","content_type":"application/pdf","file_id":"21493"}],"OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","author":[{"first_name":"Maximilian","last_name":"Hübl","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","full_name":"Hübl, Maximilian"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich"}],"day":"05","month":"03","file_date_updated":"2026-03-23T15:53:29Z","fulldoi":"https://doi.org/10.1103/68rs-3qgn","date_updated":"2026-03-23T15:59:11Z","OA_place":"publisher","date_created":"2026-03-23T14:58:31Z","publication":"Physical Review Research","has_accepted_license":"1","title":"Entropic size control of self-assembled filaments","language":[{"iso":"eng"}],"department":[{"_id":"CaGo"},{"_id":"GradSch"}],"oa":1,"article_number":"L012054","article_processing_charge":"Yes","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"ddc":["530"],"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.","doi":"10.1103/68rs-3qgn","volume":8,"quality_controlled":"1","year":"2026","status":"public","date_published":"2026-03-05T00:00:00Z","_id":"21482","intvolume":" 8","citation":{"ista":"Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments. Physical Review Research. 8, L012054.","short":"M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026).","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” Physical Review Research, vol. 8, L012054, American Physical Society, 2026, doi:10.1103/68rs-3qgn.","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” Physical Review Research. American Physical Society, 2026. https://doi.org/10.1103/68rs-3qgn.","ieee":"M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,” Physical Review Research, vol. 8. American Physical Society, 2026.","apa":"Hübl, M., & Goodrich, C. P. (2026). Entropic size control of self-assembled filaments. Physical Review Research. American Physical Society. https://doi.org/10.1103/68rs-3qgn","ama":"Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. Physical Review Research. 2026;8. doi:10.1103/68rs-3qgn"},"publication_identifier":{"eissn":["2643-1564"]},"publication_status":"published","publisher":"American Physical Society","DOAJ_listed":"1","corr_author":"1","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."}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"date_published":"2026-06-18T00:00:00Z","dataavailabilitystatement":"The data that support the findings of this article are not\r\npublicly available. The data are available from the authors\r\nupon reasonable request.","_id":"22248","PlanS_conform":"1","year":"2026","status":"public","volume":4,"quality_controlled":"1","acknowledgement":"We thank Nathan Keim, Aayush Desai, Nicholas Barton,\r\nand Gašper Tkacik for important and stimulating discussions. ˇ\r\nThe work was funded by the Institute of Science and Technology Austria.","doi":"10.1103/48k2-cw3b","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"Many living and artificial systems improve their fitness or performance by adapting to changing environments or diverse training data. However, it remains unclear how environmental variation shapes adaptation, what is learned, and when memory of past conditions is retained. Here we show how cyclic environmental change can produce robust memory. Using a model athermal disordered solid trained by inverse design to attain target elastic properties over a prescribed range, we find that the system evolves toward a marginally absorbing manifold (MAM), meaning that training is reversible within the training range but not beyond it, which encodes a memory of that range. We further propose a general mechanism for MAM formation and memory encoding based on discontinuities in the gradient of the trained quantity. These results provide a simple, broadly applicable physical framework for how adaptive systems learn under changing environments and retain memory of past conditions."}],"corr_author":"1","publication_identifier":{"eissn":["2835-8279"]},"publication_status":"published","publisher":"American Physical Society","DOAJ_listed":"1","intvolume":" 4","citation":{"short":"M. Zu, C.P. Goodrich, PRX Life 4 (2026).","ista":"Zu M, Goodrich CP. 2026. Learning by Training: Emergent physical memory from cyclically tuning disordered sphere packings. PRX Life. 4(2), 023029.","ama":"Zu M, Goodrich CP. Learning by Training: Emergent physical memory from cyclically tuning disordered sphere packings. PRX Life. 2026;4(2). doi:10.1103/48k2-cw3b","apa":"Zu, M., & Goodrich, C. P. (2026). Learning by Training: Emergent physical memory from cyclically tuning disordered sphere packings. PRX Life. American Physical Society. https://doi.org/10.1103/48k2-cw3b","ieee":"M. Zu and C. P. Goodrich, “Learning by Training: Emergent physical memory from cyclically tuning disordered sphere packings,” PRX Life, vol. 4, no. 2. American Physical Society, 2026.","chicago":"Zu, Mengjie, and Carl Peter Goodrich. “Learning by Training: Emergent Physical Memory from Cyclically Tuning Disordered Sphere Packings.” PRX Life. American Physical Society, 2026. https://doi.org/10.1103/48k2-cw3b.","mla":"Zu, Mengjie, and Carl Peter Goodrich. “Learning by Training: Emergent Physical Memory from Cyclically Tuning Disordered Sphere Packings.” PRX Life, vol. 4, no. 2, 023029, American Physical Society, 2026, doi:10.1103/48k2-cw3b."},"article_processing_charge":"Yes","department":[{"_id":"CaGo"}],"scopus_import":"1","article_number":"023029","oa":1,"language":[{"iso":"eng"}],"ddc":["570"],"date_updated":"2026-07-06T07:28:45Z","fulldoi":"https://doi.org/10.1103/48k2-cw3b","supplementarymaterial":"no","file_date_updated":"2026-07-06T07:24:43Z","researchdata_availability":"upon request","issue":"2","month":"06","has_accepted_license":"1","title":"Learning by Training: Emergent physical memory from cyclically tuning disordered sphere packings","date_created":"2026-07-05T22:01:37Z","publication":"PRX Life","OA_place":"publisher","OA_type":"gold","das_tickbox":"1","file":[{"file_name":"2026_PRXLife_Zu.pdf","date_updated":"2026-07-06T07:24:43Z","file_size":2758728,"creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","file_id":"22251","checksum":"e2d13c30bf9c036951fd2ba3455cf72a","content_type":"application/pdf","date_created":"2026-07-06T07:24:43Z"}],"article_type":"original","author":[{"last_name":"Zu","first_name":"Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","full_name":"Zu, Mengjie"},{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"day":"18","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","author":[{"full_name":"Bain, Nicolas","last_name":"Bain","first_name":"Nicolas"},{"first_name":"Lawrence A.","last_name":"Wilen","full_name":"Wilen, Lawrence A."},{"full_name":"Gerber, Dominic","last_name":"Gerber","first_name":"Dominic"},{"id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","full_name":"Zu, Mengjie","first_name":"Mengjie","last_name":"Zu"},{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Duraivel, Senthilkumar","last_name":"Duraivel","first_name":"Senthilkumar"},{"last_name":"Varma","first_name":"Kaarthik","full_name":"Varma, Kaarthik"},{"first_name":"Harsha","last_name":"Koganti","full_name":"Koganti, Harsha"},{"first_name":"Robert W.","last_name":"Style","full_name":"Style, Robert W."},{"first_name":"Eric R.","last_name":"Dufresne","full_name":"Dufresne, Eric R."}],"arxiv":1,"article_type":"original","file":[{"date_created":"2026-07-13T11:16:47Z","file_id":"22309","content_type":"application/pdf","checksum":"47354f40981223fb0c9afe292f16ead1","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2026-07-13T11:16:47Z","file_size":4367284,"file_name":"2026_PhysicalReviewX_Bain.pdf"}],"external_id":{"arxiv":["2410.09158"]},"das_tickbox":"1","OA_type":"gold","publication":"Physical Review X","date_created":"2026-07-13T09:40:54Z","OA_place":"publisher","title":"Multiscale interfacial mechanics of soft solids","has_accepted_license":"1","month":"06","issue":"2","fulldoi":"https://doi.org/10.1103/8msx-l8s7","supplementarymaterial":"yes","date_updated":"2026-07-13T11:17:51Z","researchdata_availability":"yes","file_date_updated":"2026-07-13T11:16:47Z","ddc":["530"],"language":[{"iso":"eng"}],"article_processing_charge":"Yes","article_number":"021063","oa":1,"department":[{"_id":"CaGo"}],"scopus_import":"1","DOAJ_listed":"1","publication_status":"published","publisher":"American Physical Society","publication_identifier":{"issn":["2160-3308"]},"citation":{"short":"N. Bain, L.A. Wilen, D. Gerber, M. Zu, C.P. Goodrich, S. Duraivel, K. Varma, H. Koganti, R.W. Style, E.R. Dufresne, Physical Review X 16 (2026).","ista":"Bain N, Wilen LA, Gerber D, Zu M, Goodrich CP, Duraivel S, Varma K, Koganti H, Style RW, Dufresne ER. 2026. Multiscale interfacial mechanics of soft solids. Physical Review X. 16(2), 021063.","chicago":"Bain, Nicolas, Lawrence A. Wilen, Dominic Gerber, Mengjie Zu, Carl Peter Goodrich, Senthilkumar Duraivel, Kaarthik Varma, Harsha Koganti, Robert W. Style, and Eric R. Dufresne. “Multiscale Interfacial Mechanics of Soft Solids.” Physical Review X. American Physical Society, 2026. https://doi.org/10.1103/8msx-l8s7.","ieee":"N. Bain et al., “Multiscale interfacial mechanics of soft solids,” Physical Review X, vol. 16, no. 2. American Physical Society, 2026.","mla":"Bain, Nicolas, et al. “Multiscale Interfacial Mechanics of Soft Solids.” Physical Review X, vol. 16, no. 2, 021063, American Physical Society, 2026, doi:10.1103/8msx-l8s7.","apa":"Bain, N., Wilen, L. A., Gerber, D., Zu, M., Goodrich, C. P., Duraivel, S., … Dufresne, E. R. (2026). Multiscale interfacial mechanics of soft solids. Physical Review X. American Physical Society. https://doi.org/10.1103/8msx-l8s7","ama":"Bain N, Wilen LA, Gerber D, et al. Multiscale interfacial mechanics of soft solids. Physical Review X. 2026;16(2). doi:10.1103/8msx-l8s7"},"intvolume":" 16","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","abstract":[{"text":"Soft solids and their surface deformations control the response of many natural and artificial systems. Yet, their underlying properties are vigorously debated, particularly for polymer networks. While molecular-scale theories predict no interfacial changes with macroscopic deformation, multiple experiments suggest otherwise. To settle this issue, we measure displacement fields near the interface of a silicone gel, in the limit of small deformations. We discover an unexpected multiscale response. The shear modulus decreases smoothly by half with 20  μ⁢m of the interface. At the same time we observe a surface excess elasticity, that depends on history and outer medium composition. These results reveal the fundamentally multiscale nature of polymeric surfaces, and call for further experimental and theoretical investigations into the basic understanding of soft solid interfaces.","lang":"eng"}],"volume":16,"quality_controlled":"1","doi":"10.1103/8msx-l8s7","acknowledgement":"The authors thank Katharine Jensen, Stefanie Heyden, Thomas Salez, Francesco Stellacci, Denis Bartolo, Francesco Picella, Hélène Delanoë-Ayari, Mathieu Leocmach, Antoine Bérut, Cécile Cottin-Bizonne, Anne-Laure Biance, and Oriane Talabart for useful discussions. We also thank the reviewers for excellent suggestions that substantively improved the manuscript.","PlanS_conform":"1","_id":"22288","dataavailabilitystatement":"The data that support the findings of this article are openly available https://github.com/nicobain/Multiscale_interfacial_mechanics_soft_solids_data","date_published":"2026-06-30T00:00:00Z","status":"public","year":"2026"},{"file_date_updated":"2026-07-27T10:57:57Z","researchdata_availability":"yes","supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1038/s41567-025-03120-3","date_updated":"2026-07-27T10:59:15Z","month":"02","has_accepted_license":"1","title":"A polyhedral structure controls programmable self-assembly","OA_place":"publisher","publication":"Nature Physics","date_created":"2026-01-20T10:02:19Z","OA_type":"hybrid","das_tickbox":"1","article_type":"original","file":[{"date_created":"2026-07-27T10:57:57Z","file_id":"22417","content_type":"application/pdf","checksum":"f4e3123d5d9dfcd22324e2c2de02e9a2","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2026_NaturePhysics_Huebl.pdf","date_updated":"2026-07-27T10:57:57Z","file_size":2802534}],"author":[{"id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","full_name":"Hübl, Maximilian","last_name":"Hübl","first_name":"Maximilian"},{"last_name":"Videbæk","first_name":"Thomas E.","full_name":"Videbæk, Thomas E."},{"full_name":"Hayakawa, Daichi","first_name":"Daichi","last_name":"Hayakawa"},{"first_name":"W. Benjamin","last_name":"Rogers","full_name":"Rogers, W. Benjamin"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"}],"day":"01","page":"294-301","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://ista.ac.at/en/news/behind-natures-blueprints/","description":"News on ISTA website","relation":"press_release"}]},"type":"journal_article","year":"2026","status":"public","dataavailabilitystatement":"Design files and folding conditions of DNA origami used in this work are provided in the repository Nanobase68 and are accessible at https://nanobase.org/structures/247. All the TEM images and associated experimental data are available via Zenodo at https://doi.org/10.5281/zenodo.17314727 (ref. 70).\r\nStructure enumeration was performed using the Roly.jl27,71 (v.0.1.0) package developed by M.C.H. and C.P.G., which is available via GitHub at https://github.com/mxhbl/Roly.jl. Polyhedral computation and linear programming were performed using the freely available Convex.jl72 (v.0.16.4) package, Polyhedra.jl73 (v.0.7.8) package and cddlib63 (v.0.9.4) library. The example code reproducing the calculations done on the three rings and reconfigurable squares is available via GitHub at https://github.com/mxhbl/PolyhedralStructureOfSelfAssembly. An implementation of the lattice Monte Carlo sampler is available via GitHub at https://github.com/mxhbl/LatticeSampler. Fitting of the yield curves was achieved using the freely available Optim.jl74 (v.1.12.0) package.","date_published":"2026-02-01T00:00:00Z","_id":"21006","PlanS_conform":"1","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","volume":22,"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"corr_author":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 22","citation":{"ama":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. A polyhedral structure controls programmable self-assembly. Nature Physics. 2026;22:294-301. doi:10.1038/s41567-025-03120-3","apa":"Hübl, M., Videbæk, T. E., Hayakawa, D., Rogers, W. B., & Goodrich, C. P. (2026). A polyhedral structure controls programmable self-assembly. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03120-3","chicago":"Hübl, Maximilian, Thomas E. Videbæk, Daichi Hayakawa, W. Benjamin Rogers, and Carl Peter Goodrich. “A Polyhedral Structure Controls Programmable Self-Assembly.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-025-03120-3.","mla":"Hübl, Maximilian, et al. “A Polyhedral Structure Controls Programmable Self-Assembly.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 294–301, doi:10.1038/s41567-025-03120-3.","ieee":"M. Hübl, T. E. Videbæk, D. Hayakawa, W. B. Rogers, and C. P. Goodrich, “A polyhedral structure controls programmable self-assembly,” Nature Physics, vol. 22. Springer Nature, pp. 294–301, 2026.","short":"M. Hübl, T.E. Videbæk, D. Hayakawa, W.B. Rogers, C.P. Goodrich, Nature Physics 22 (2026) 294–301.","ista":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. 2026. A polyhedral structure controls programmable self-assembly. Nature Physics. 22, 294–301."},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"scopus_import":"1","oa":1,"project":[{"_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","grant_number":"FTI23-G-011","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks"}],"article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"ddc":["570","540"]},{"year":"2026","status":"public","date_published":"2026-07-15T00:00:00Z","PlanS_conform":"1","_id":"22645","acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and the Lab Support Facility (LSF). M.E. acknowledges financial support from Deutsche Forschungsgemeinschaft through Collaborative Research Centre 1411. We thank Dr. Tommaso Constanzo and Tobias Kleinhanns for assistance with high-quality electron microscope image acquisition, Dr. Jeonghyun Park for providing NCs, Dr. Mariano Calcabrini for assistance with the NMR study, and Prof. Jonathan De Roo for fruitful discussions. This work benefited from the use of the SasView application, originally developed under NSF award DMR-0520547. SasView contains code developed with funding from the European Union’s Horizon 2020 research and innovation program under the SINE2020 project, grant agreement No. 654000.","doi":"10.1021/jacs.6c07859","quality_controlled":"1","volume":148,"abstract":[{"text":"Nanocrystal superlattices are commonly formed by changing concentration, solvent conditions, or particle surface chemistry. Although effective, these approaches alter multiple contributions to the interparticle potential simultaneously, making it difficult to isolate the interactions responsible for ordering or to control assembly in chemically complex environments. Here, we show that oligomeric species present in a nanocrystal reaction medium drive superlattice formation through a depletion mechanism. Using PbTe nanocrystals as a model system, we identify Pb–oleate oligomers in the crude reaction mixture, characterize their solution structure, and quantify their contribution to the interparticle potential, establishing depletion as the dominant short-range interaction governing spontaneous body-centered cubic superlattice formation. We then confirm the depletion origin of ordering by showing that varying depletant concentration predictably shifts the order–disorder boundary and produces a thermally reversible transition between dispersed and ordered states ─ behavior that is inconsistent with van der Waals or ligand-mediated mechanisms but is a direct consequence of depletion control. Having established and validated the mechanism, we demonstrate that the same depletion framework can be deliberately activated in purified dispersions and transferred across nanocrystal systems of different composition and shape, including anisotropic and binary assemblies. These results establish precursor-derived depletion as a general and chemically grounded mechanism for nanocrystal superlattice formation, and show that collective ordering can be programmed through the surrounding medium rather than through particle surface modification.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 148","citation":{"ama":"Lee S, Balazs D, Rayaroth Puthiyaveettil A, et al. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 2026;148(29):31245-31252. doi:10.1021/jacs.6c07859","apa":"Lee, S., Balazs, D., Rayaroth Puthiyaveettil, A., Horta, S., Goodrich, C. P., Engel, M., … Ibáñez, M. (2026). Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. American Chemical Society. https://doi.org/10.1021/jacs.6c07859","ieee":"S. Lee et al., “Reaction medium asan architect of nanocrystal superlattices,” Journal of the AmericanChemical Society, vol. 148, no. 29. American Chemical Society, pp. 31245–31252, 2026.","mla":"Lee, Seungho, et al. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society, vol. 148, no. 29, American Chemical Society, 2026, pp. 31245–52, doi:10.1021/jacs.6c07859.","chicago":"Lee, Seungho, Daniel Balazs, Aiswarya Rayaroth Puthiyaveettil, Sharona Horta, Carl Peter Goodrich, Michael Engel, Ihor Cherniukh, and Maria Ibáñez. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c07859.","ista":"Lee S, Balazs D, Rayaroth Puthiyaveettil A, Horta S, Goodrich CP, Engel M, Cherniukh I, Ibáñez M. 2026. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 148(29), 31245–31252.","short":"S. Lee, D. Balazs, A. Rayaroth Puthiyaveettil, S. Horta, C.P. Goodrich, M. Engel, I. Cherniukh, M. Ibáñez, Journal of the AmericanChemical Society 148 (2026) 31245–31252."},"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","publisher":"American Chemical Society","scopus_import":"1","department":[{"_id":"MaIb"},{"_id":"LifeSc"},{"_id":"GradSch"},{"_id":"CaGo"}],"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"article_processing_charge":"Yes (via OA deal)","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"pmid":1,"language":[{"iso":"eng"}],"ddc":["540"],"file_date_updated":"2026-08-04T06:40:17Z","researchdata_availability":"no","fulldoi":"https://doi.org/10.1021/jacs.6c07859","date_updated":"2026-08-04T06:47:13Z","supplementarymaterial":"yes","issue":"29","month":"07","has_accepted_license":"1","title":"Reaction medium asan architect of nanocrystal superlattices","OA_place":"publisher","date_created":"2026-08-04T06:29:31Z","publication":"Journal of the AmericanChemical Society","das_tickbox":"0","OA_type":"hybrid","external_id":{"pmid":["42532904"]},"file":[{"date_created":"2026-08-04T06:40:17Z","checksum":"063314ae5ac4225ebd4436aa8707d113","content_type":"application/pdf","file_id":"22646","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"file_size":6564594,"date_updated":"2026-08-04T06:40:17Z","file_name":"2026_JACS_Lee.pdf"}],"article_type":"original","author":[{"last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X"},{"id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","full_name":"Rayaroth Puthiyaveettil, Aiswarya","last_name":"Rayaroth Puthiyaveettil","first_name":"Aiswarya"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona","last_name":"Horta","first_name":"Sharona"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Michael","last_name":"Engel","full_name":"Engel, Michael"},{"full_name":"Cherniukh, Ihor","id":"d03b62b2-5976-11ef-a8d7-9525504b7895","first_name":"Ihor","last_name":"Cherniukh"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez"}],"day":"15","page":"31245-31252","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"keyword":["functional nanostructures","bistability","target behavior","transition 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Andreas","first_name":"Andreas","last_name":"Ehrmann"}],"month":"09","file_date_updated":"2026-09-08T18:36:14Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-22852","date_updated":"2026-09-09T07:24:10Z","OA_place":"repository","date_created":"2026-09-08T11:32:53Z","has_accepted_license":"1","title":"Supplemental videos for Designing bistable nanostructures for target behavior","department":[{"_id":"GradSch"},{"_id":"CaGo"},{"_id":"EdHa"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"article_processing_charge":"No","project":[{"grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids","_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d"}],"doi":"10.15479/AT-ISTA-22852","doi_confirm":"1","year":"2026","status":"public","date_published":"2026-09-09T00:00:00Z","_id":"22852","citation":{"ista":"Ehrmann A. 2026. Supplemental videos for Designing bistable nanostructures for target behavior, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22852.","short":"A. Ehrmann, (2026).","ama":"Ehrmann A. Supplemental videos for Designing bistable nanostructures for target behavior. 2026. doi:10.15479/AT-ISTA-22852","apa":"Ehrmann, A. (2026). Supplemental videos for Designing bistable nanostructures for target behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22852","mla":"Ehrmann, Andreas. Supplemental Videos for Designing Bistable Nanostructures for Target Behavior. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22852.","chicago":"Ehrmann, Andreas. “Supplemental Videos for Designing Bistable Nanostructures for Target Behavior.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22852.","ieee":"A. Ehrmann, “Supplemental videos for Designing bistable nanostructures for target behavior.” Institute of Science and Technology Austria, 2026."},"publisher":"Institute of Science and Technology Austria","contributor":[{"orcid":"0000-0002-0997-5678","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","contributor_type":"data_collector","first_name":"Andreas","last_name":"Ehrmann"}],"corr_author":"1","abstract":[{"text":"This Research Data contains supplemental videos for Chapter 4 \"Designing bistable nanostructures for target behavior\" of my PhD Thesis \"Biological functionality without biochemistry: designing nanomachines for target behavior\".\r\nSupplemental video 1: Video showing the transition pathway of a bistable nanostructure with sphere-based arms, corresponding to the Machine in Scenario 4.\r\nSupplemental video 2: Video showing the transition pathway of the Source in Scenario 1. The arm tips change sides during the transition, demonstrating that the arms pass through each other.\r\nSupplemental video 3: Video showing the transition pathway of a fully polyhedral hinge structure with unconstrained arms. Note that we only show the ends of the arms.\r\nSupplemental video 4: Video showing the transition pathway of the coupled energy-delivery reaction of a Machine (gray) and a Source (blue) nanostructure for the optimized parameters in Scenario 3. Note that we only show the ends of the arms.","lang":"eng"}],"oa_version":"None","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"}},{"language":[{"iso":"eng"}],"project":[{"_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","name":"Functional bio-inspired nanomachines from sticky colloids","grant_number":"PAT 8537123"}],"article_processing_charge":"No","department":[{"_id":"CaGo"},{"_id":"EdHa"},{"_id":"AnSa"}],"oa":1,"publication_status":"draft","citation":{"ieee":"A. Ehrmann, M. Krstić, S. Samadzadeh, and C. P. Goodrich, “Designing bistable nanostructures for target behavior,” arXiv. .","mla":"Ehrmann, Andreas, et al. “Designing Bistable Nanostructures for Target Behavior.” ArXiv, doi:10.48550/arXiv.2606.31620.","chicago":"Ehrmann, Andreas, Marija Krstić, Sahar Samadzadeh, and Carl Peter Goodrich. “Designing Bistable Nanostructures for Target Behavior.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2606.31620.","ama":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv. doi:10.48550/arXiv.2606.31620","apa":"Ehrmann, A., Krstić, M., Samadzadeh, S., & Goodrich, C. P. (n.d.). Designing bistable nanostructures for target behavior. arXiv. https://doi.org/10.48550/arXiv.2606.31620","short":"A. Ehrmann, M. Krstić, S. Samadzadeh, C.P. Goodrich, ArXiv (n.d.).","ista":"Ehrmann A, Krstić M, Samadzadeh S, Goodrich CP. Designing bistable nanostructures for target behavior. arXiv, 10.48550/arXiv.2606.31620."},"oa_version":"Preprint","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"abstract":[{"lang":"eng","text":"Many biological machines function through controlled conformational transitions, yet designing synthetic nanostructures with prescribed dynamical behavior remains a major challenge. Here, we develop a modular inverse-design framework for bistable nanostructures whose function is controlled by an energy profile along a geometric reaction coordinate. Inspired by proteins with rigid domains connected by flexible hinges, we introduce a hinge-arm paradigm in which a small bistable hinge controls the energetics of a conformational transition, while rigid arms map this transition onto the separation between external binding sites. Specifically, we ask which features of a target energy profile can be programmed under different design constraints. We find that the energy barriers and the binding-site separations in the two metastable states can be readily designed, while controlling the location of the transition state or the full shape of the energy profile requires additional design freedom. Using a differentiable design framework, we find that some optimized solutions are numerically inexact but still display the functional behavior for which the target profile was selected, emphasizing the importance of function-based evaluation criteria. These results establish a practical hierarchy of designability for bistable nanostructures and provide a route toward synthetic nanomachines that couple conformational transitions to target behavior."}],"corr_author":"1","acknowledgement":"We thank Maitane Muñoz-Basagoiti for stimulating\r\ndiscussions. This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].\r\n","doi":"10.48550/arXiv.2606.31620","date_published":"2026-06-30T00:00:00Z","_id":"22893","year":"2026","status":"public","type":"preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"22873","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-0997-5678","full_name":"Ehrmann, Andreas","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","first_name":"Andreas","last_name":"Ehrmann"},{"last_name":"Krstić","first_name":"Marija","id":"a8f6d1c6-3200-11ee-973b-dab948eace26","full_name":"Krstić, Marija"},{"first_name":"Sahar","last_name":"Samadzadeh","id":"0099896b-5fb8-11ef-8420-b30b14627e93","full_name":"Samadzadeh, Sahar"},{"last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"day":"30","arxiv":1,"external_id":{"arxiv":["2606.31620"]},"OA_type":"green","publication":"arXiv","date_created":"2026-09-09T13:19:13Z","OA_place":"repository","title":"Designing bistable nanostructures for target behavior","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2606.31620"}],"month":"06","fulldoi":"https://doi.org/10.48550/arXiv.2606.31620","date_updated":"2026-09-18T11:28:28Z"},{"oa_version":"Preprint","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"abstract":[{"lang":"eng","text":"Countless biological processes are fueled by energy-rich molecules like ATP and GTP that supply energy with extreme efficiency. However, designing similar energy-delivery schemes from the bottom up, essential for the development of powered nanostructures and other \\emph{de novo} machinery, presents a significant challenge: how can an energy-rich structure be stable in solution yet still deliver this energy at precisely the right time? In this paper, we present a purely physical mechanism that solves this challenge, facilitating energy transfer akin to ATP hydrolysis, yet occurring between synthetic nanostructures without any biochemical interactions. This targeted energy delivery is achieved by exploiting a differentiable state-based model to balance the energy profiles that govern the structural transitions in the two nanostructures, creating a coupled relaxation pathway with minimal barriers that facilitates energy delivery. We verify the effectiveness and robustness of this mechanism through Langevin Dynamics simulations, demonstrating that a bath of the high-energy structures can systematically and repeatedly drive the target structure out of equilibrium, enabling it to perform tasks. As the mechanism operates only through explicit physical forces without any biochemistry or internal state variables, our results present generic and far-reaching design principles, setting the stage for the next generation of synthetic nanomachines."}],"corr_author":"1","publication_status":"draft","citation":{"apa":"Ehrmann, A., & Goodrich, C. P. (n.d.). Controlling energy delivery with bistable nanostructures. arXiv. https://doi.org/10.48550/arXiv.2506.14266","ama":"Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. arXiv. doi:10.48550/arXiv.2506.14266","chicago":"Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2506.14266.","mla":"Ehrmann, Andreas, and Carl Peter Goodrich. “Controlling Energy Delivery with Bistable Nanostructures.” ArXiv, doi:10.48550/arXiv.2506.14266.","ieee":"A. Ehrmann and C. P. Goodrich, “Controlling energy delivery with bistable nanostructures,” arXiv. .","short":"A. Ehrmann, C.P. Goodrich, ArXiv (n.d.).","ista":"Ehrmann A, Goodrich CP. Controlling energy delivery with bistable nanostructures. arXiv, 10.48550/arXiv.2506.14266."},"date_published":"2026-06-07T00:00:00Z","_id":"22892","year":"2026","status":"public","acknowledgement":"We thank Edouard Hannezo, Ella King, Maximilian Lechner, and Jérémie Palacci for stimulating discussions, and Edouard Hannezo, Maximilian Hübl, and\r\nMaitane Muñoz-Basagoiti for helpful comments on the manuscript. This research was funded in part by the\r\nAustrian Science Fund (FWF) [10.55776/PAT8537123].","doi":"10.48550/arXiv.2506.14266","project":[{"_id":"90a98bb5-16d5-11f0-9cad-9675f3f8015d","grant_number":"PAT 8537123","name":"Functional bio-inspired nanomachines from sticky colloids"}],"article_processing_charge":"No","department":[{"_id":"CaGo"},{"_id":"EdHa"}],"oa":1,"language":[{"iso":"eng"}],"title":"Controlling energy delivery with bistable nanostructures","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2506.14266","open_access":"1"}],"publication":"arXiv","date_created":"2026-09-09T13:16:54Z","OA_place":"repository","fulldoi":"https://doi.org/10.48550/arXiv.2506.14266","date_updated":"2026-09-18T11:28:29Z","month":"06","day":"07","author":[{"first_name":"Andreas","last_name":"Ehrmann","id":"eaa689ed-f6e0-11ea-865d-bd98cbcf83c2","orcid":"0000-0002-0997-5678","full_name":"Ehrmann, Andreas"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"}],"arxiv":1,"type":"preprint","related_material":{"record":[{"status":"public","id":"22873","relation":"dissertation_contains"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2506.14266"]}},{"doi_confirm":"1","doi":"10.15479/AT-ISTA-22873","acknowledgement":"I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123].","alternative_title":["ISTA Thesis"],"_id":"22873","date_published":"2026-09-04T00:00:00Z","status":"public","year":"2026","publication_status":"published","publisher":"Institute of Science and Technology Austria","publication_identifier":{"isbn":["978-3-99078-092-3"],"issn":["2663-337X"]},"citation":{"mla":"Ehrmann, Andreas. Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22873.","ieee":"A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.","chicago":"Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22873.","ama":"Ehrmann A. Biological functionality without biochemistry: Designing nanomachines for target behavior. 2026. doi:10.15479/AT-ISTA-22873","apa":"Ehrmann, A. (2026). Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22873","short":"A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026.","ista":"Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. 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Carmen","full_name":"Miguel, M. Carmen"},{"first_name":"Maria Jose","last_name":"Esplandiu","full_name":"Esplandiu, Maria Jose"},{"last_name":"Simmchen","first_name":"Juliane","full_name":"Simmchen, Juliane"},{"first_name":"Wolfgang J.","last_name":"Parak","full_name":"Parak, Wolfgang J."},{"first_name":"Marco","last_name":"Werner","full_name":"Werner, Marco"},{"last_name":"Gompper","first_name":"Gerhard","full_name":"Gompper, Gerhard"},{"last_name":"Hanczyc","first_name":"Martin M.","full_name":"Hanczyc, Martin M."}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["40358970"]},"OA_type":"green","article_type":"review","oa_version":"Submitted Version","abstract":[{"text":"Intelligent soft matter lies at the intersection of materials science, physics, and cognitive science, promising to change how we design and interact with materials. This transformative field aims to create materials with life-like capabilities, such as perception, learning, memory, and adaptive behavior. Unlike traditional materials, which typically perform static or predefined functions, intelligent soft matter can dynamically interact with its environment, integrating multiple sensory inputs, retaining past experiences, and making decisions to optimize its responses. Inspired by biological systems, these materials leverage the inherent properties of soft matter such as flexibility, adaptability, and responsiveness to perform functions that mimic cognitive processes. By synthesizing current research trends and projecting their evolution, we present a forward-looking perspective on how intelligent soft matter could be constructed, with the aim of inspiring innovations in areas such as biomedical devices, adaptive robotics, and beyond. We highlight new pathways for integrating sensing, memory and actuation with low-power internal operations, and we discuss key challenges in realizing materials that exhibit truly “intelligent behavior”. These approaches outline a path toward more robust, versatile, and scalable materials that can potentially act, compute, and “think” through their inherent intrinsic material properties—moving beyond traditional smart technologies that rely on external control.","lang":"eng"}],"publication_status":"published","publisher":"Royal Society of Chemistry","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"short":"V.A. Baulin, A. Giacometti, D.A. Fedosov, S. Ebbens, N.R. Varela-Rosales, N. Feliu, M. Chowdhury, M. Hu, R. Füchslin, M. Dijkstra, M. Mussel, R. van Roij, D. Xie, V. Tzanov, M. Zu, S. Hidalgo-Caballero, Y. Yuan, L. Cocconi, C.-M. Ghim, C. Cottin-Bizonne, M.C. Miguel, M.J. Esplandiu, J. Simmchen, W.J. Parak, M. Werner, G. Gompper, M.M. Hanczyc, Soft Matter (2025) 4129–4145.","ista":"Baulin VA, Giacometti A, Fedosov DA, Ebbens S, Varela-Rosales NR, Feliu N, Chowdhury M, Hu M, Füchslin R, Dijkstra M, Mussel M, van Roij R, Xie D, Tzanov V, Zu M, Hidalgo-Caballero S, Yuan Y, Cocconi L, Ghim C-M, Cottin-Bizonne C, Miguel MC, Esplandiu MJ, Simmchen J, Parak WJ, Werner M, Gompper G, Hanczyc MM. 2025. Intelligent soft matter: Towards embodied intelligence. Soft Matter. (21), 4129–4145.","ama":"Baulin VA, Giacometti A, Fedosov DA, et al. Intelligent soft matter: Towards embodied intelligence. Soft Matter. 2025;(21):4129-4145. doi:10.1039/d5sm00174a","apa":"Baulin, V. A., Giacometti, A., Fedosov, D. A., Ebbens, S., Varela-Rosales, N. R., Feliu, N., … Hanczyc, M. M. (2025). Intelligent soft matter: Towards embodied intelligence. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d5sm00174a","mla":"Baulin, Vladimir A., et al. “Intelligent Soft Matter: Towards Embodied Intelligence.” Soft Matter, no. 21, Royal Society of Chemistry, 2025, pp. 4129–45, doi:10.1039/d5sm00174a.","chicago":"Baulin, Vladimir A., Achille Giacometti, Dmitry A. Fedosov, Stephen Ebbens, Nydia R. Varela-Rosales, Neus Feliu, Mithun Chowdhury, et al. “Intelligent Soft Matter: Towards Embodied Intelligence.” Soft Matter. Royal Society of Chemistry, 2025. https://doi.org/10.1039/d5sm00174a.","ieee":"V. A. Baulin et al., “Intelligent soft matter: Towards embodied intelligence,” Soft Matter, no. 21. Royal Society of Chemistry, pp. 4129–4145, 2025."},"_id":"21237","date_published":"2025-06-07T00:00:00Z","status":"public","year":"2025","quality_controlled":"1","doi":"10.1039/d5sm00174a","acknowledgement":"The work is the result of the SoftComp Topical workshop on Intelligent Soft Matter, Salou 2025 (https://softmat.net/intelligent-soft-matter/) financed by SoftComp Network of Excellence (https://eu-softcomp.net/). Various AI tools were used for preparation of the manuscript: language models Google Gemini 2.0 series and Discovery Engine (https://explore-the-unknown.vercel.app) for literature processing, structuring contributions, finding concept overlaps and summarizing according to procedure explained in https://github.com/vbaulin/IntelliDE/.","article_processing_charge":"No","oa":1,"department":[{"_id":"CaGo"}],"language":[{"iso":"eng"}],"pmid":1},{"title":"Accessing semiaddressable self-assembly with efficient structure enumeration","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.13567"}],"date_created":"2025-02-23T23:01:55Z","publication":"Physical Review Letters","OA_place":"repository","fulldoi":"https://doi.org/10.1103/PhysRevLett.134.058204","date_updated":"2025-09-30T10:35:47Z","issue":"5","month":"02","day":"07","author":[{"full_name":"Hübl, Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl","first_name":"Maximilian"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","first_name":"Carl Peter"}],"arxiv":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"relation":"software","url":"https://github.com/mxhbl/Roly.jl"}]},"external_id":{"arxiv":["2405.13567"],"isi":["001454696800003"],"pmid":["39983190"]},"OA_type":"green","article_type":"original","oa_version":"Preprint","corr_author":"1","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publisher":"American Physical Society","publication_status":"published","intvolume":" 134","citation":{"short":"M. Hübl, C.P. Goodrich, Physical Review Letters 134 (2025).","ista":"Hübl M, Goodrich CP. 2025. Accessing semiaddressable self-assembly with efficient structure enumeration. Physical Review Letters. 134(5), 058204.","ieee":"M. Hübl and C. P. Goodrich, “Accessing semiaddressable self-assembly with efficient structure enumeration,” Physical Review Letters, vol. 134, no. 5. American Physical Society, 2025.","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly with Efficient Structure Enumeration.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.058204.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly with Efficient Structure Enumeration.” Physical Review Letters, vol. 134, no. 5, 058204, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.058204.","ama":"Hübl M, Goodrich CP. Accessing semiaddressable self-assembly with efficient structure enumeration. Physical Review Letters. 2025;134(5). doi:10.1103/PhysRevLett.134.058204","apa":"Hübl, M., & Goodrich, C. P. (2025). Accessing semiaddressable self-assembly with efficient structure enumeration. Physical Review Letters. 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The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","doi":"10.1103/PhysRevLett.134.058204","isi":1,"article_processing_charge":"No","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"scopus_import":"1","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"oa":1,"article_number":"058204","language":[{"iso":"eng"}],"pmid":1},{"OA_type":"hybrid","external_id":{"arxiv":["2412.05031"],"isi":["001509005900006"]},"file":[{"creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2025-06-23T11:41:08Z","file_size":1132625,"file_name":"2025_PhysReviewLetters_Zu.pdf","date_created":"2025-06-23T11:41:08Z","content_type":"application/pdf","checksum":"040b6779c91aac62c15a9b2cc417b360","file_id":"19874"}],"article_type":"original","arxiv":1,"author":[{"id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","full_name":"Zu, Mengjie","last_name":"Zu","first_name":"Mengjie"},{"last_name":"Desai","first_name":"Aayush A","id":"502cfd30-32c1-11ee-a9a4-d8dad5c6739e","full_name":"Desai, Aayush A"},{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"}],"day":"13","related_material":{"link":[{"url":"https://ista.ac.at/en/news/infinite-diversity-in-infinite-combinations/","description":"News on ISTA website","relation":"press_release"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"journal_article","file_date_updated":"2025-06-23T11:41:08Z","date_updated":"2026-04-28T13:28:02Z","fulldoi":"https://doi.org/10.1103/PhysRevLett.134.238201","month":"06","issue":"23","title":"Fully independent response in disordered solids","has_accepted_license":"1","OA_place":"publisher","date_created":"2025-06-22T22:02:06Z","publication":"Physical Review Letters","article_number":"238201","oa":1,"department":[{"_id":"CaGo"},{"_id":"IlCa"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"ddc":["530"],"isi":1,"status":"public","year":"2025","_id":"19856","date_published":"2025-06-13T00:00:00Z","doi":"10.1103/PhysRevLett.134.238201","acknowledgement":"We gratefully acknowledge Edouard Hannezo for helpful comments on the manuscript. The work was funded by the Institute of Science and Technology Austria.","volume":134,"quality_controlled":"1","corr_author":"1","abstract":[{"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.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ama":"Zu M, Desai AA, Goodrich CP. Fully independent response in disordered solids. Physical Review Letters. 2025;134(23). doi:10.1103/PhysRevLett.134.238201","apa":"Zu, M., Desai, A. A., & Goodrich, C. P. (2025). Fully independent response in disordered solids. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.238201","ieee":"M. Zu, A. A. Desai, and C. P. Goodrich, “Fully independent response in disordered solids,” Physical Review Letters, vol. 134, no. 23. American Physical Society, 2025.","mla":"Zu, Mengjie, et al. “Fully Independent Response in Disordered Solids.” Physical Review Letters, vol. 134, no. 23, 238201, American Physical Society, 2025, doi:10.1103/PhysRevLett.134.238201.","chicago":"Zu, Mengjie, Aayush A Desai, and Carl Peter Goodrich. “Fully Independent Response in Disordered Solids.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.238201.","short":"M. Zu, A.A. Desai, C.P. Goodrich, Physical Review Letters 134 (2025).","ista":"Zu M, Desai AA, Goodrich CP. 2025. Fully independent response in disordered solids. Physical Review Letters. 134(23), 238201."},"intvolume":" 134","publication_status":"published","publisher":"American Physical Society","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"article_type":"original","file":[{"checksum":"c40dc4c909724b9d1146636612e8821a","content_type":"application/pdf","file_id":"20744","date_created":"2025-12-09T12:45:53Z","file_size":10621381,"file_name":"2025_PNAS_Shi.pdf","date_updated":"2025-12-09T12:45:53Z","relation":"main_file","access_level":"open_access","creator":"dernst","success":1}],"OA_type":"hybrid","external_id":{"arxiv":["2507.01739"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/science-is-like-magic-just-real/"}],"record":[{"status":"public","id":"20749","relation":"research_data"}]},"type":"journal_article","arxiv":1,"page":"e2516865122","author":[{"first_name":"Sue","last_name":"Shi","id":"5c5b9247-15b2-11ec-abd3-fd958715639c","full_name":"Shi, Sue"},{"full_name":"Hübl, Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl","first_name":"Maximilian"},{"last_name":"Grosjean","first_name":"Galien M","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"day":"16","month":"12","issue":"50","file_date_updated":"2025-12-09T12:45:53Z","fulldoi":"https://doi.org/10.1073/pnas.2516865122","date_updated":"2026-05-20T08:41:15Z","OA_place":"publisher","publication":"Proceedings of the National Academy of Sciences","date_created":"2025-12-07T23:02:00Z","title":"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter","has_accepted_license":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"department":[{"_id":"ScWa"},{"_id":"CaGo"}],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","project":[{"grant_number":"FTI23-G-011","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"ddc":["530"],"doi":"10.1073/pnas.2516865122","APC_amount":"5599.52 EUR","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.","quality_controlled":"1","volume":122,"status":"public","year":"2025","_id":"20727","date_published":"2025-12-16T00:00:00Z","citation":{"apa":"Shi, S., Hübl, M., Grosjean, G. M., Goodrich, C. P., & Waitukaitis, S. R. (2025). Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2516865122","ama":"Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. 2025;122(50):e2516865122. doi:10.1073/pnas.2516865122","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,” Proceedings of the National Academy of Sciences, 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.” Proceedings of the National Academy of Sciences, vol. 122, no. 50, National Academy of Sciences, 2025, p. e2516865122, doi:10.1073/pnas.2516865122.","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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2516865122.","short":"S. Shi, M. Hübl, G.M. Grosjean, C.P. Goodrich, S.R. Waitukaitis, Proceedings of the National Academy of Sciences 122 (2025) e2516865122.","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."},"intvolume":" 122","publisher":"National Academy of Sciences","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"corr_author":"1","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"}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version"},{"article_processing_charge":"No","oa":1,"department":[{"_id":"ScWa"},{"_id":"CaGo"}],"OA_type":"green","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20727"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"author":[{"first_name":"Sue","last_name":"Shi","full_name":"Shi, Sue","id":"5c5b9247-15b2-11ec-abd3-fd958715639c"}],"day":"10","month":"11","doi":"10.5281/ZENODO.15752991","_id":"20749","fulldoi":"https://doi.org/10.5281/ZENODO.15752991","date_updated":"2026-05-20T08:41:14Z","date_published":"2025-11-10T00:00:00Z","status":"public","year":"2025","publisher":"Zenodo","date_created":"2025-12-09T13:36:16Z","citation":{"short":"S. Shi, (2025).","ista":"Shi S. 2025. Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter’, Zenodo, 10.5281/ZENODO.15752991.","ama":"Shi S. Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” 2025. doi:10.5281/ZENODO.15752991","apa":"Shi, S. (2025). Datasets and code for manuscript “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.” Zenodo. https://doi.org/10.5281/ZENODO.15752991","chicago":"Shi, Sue. “Datasets and Code for Manuscript ‘Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.’” Zenodo, 2025. https://doi.org/10.5281/ZENODO.15752991.","ieee":"S. Shi, “Datasets and code for manuscript ‘Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter.’” Zenodo, 2025.","mla":"Shi, Sue. Datasets and Code for Manuscript “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” Zenodo, 2025, doi:10.5281/ZENODO.15752991."},"OA_place":"repository","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.15752991","open_access":"1"}],"corr_author":"1","abstract":[{"text":"Datasets and code for publication \"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter\"","lang":"eng"}],"contributor":[{"id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","first_name":"Maximilian","last_name":"Hübl"},{"orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean","first_name":"Galien M"}],"title":"Datasets and code for manuscript \"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter\"","has_accepted_license":"1"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","author":[{"id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","full_name":"Zu, Mengjie","last_name":"Zu","first_name":"Mengjie"},{"first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"arxiv":1,"file":[{"file_name":"2024_CommMaterials_Zu.pdf","file_size":9824134,"date_updated":"2024-08-12T07:56:38Z","relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"17416","content_type":"application/pdf","checksum":"d6f74e242db5f46bb0e380ee23a268af","date_created":"2024-08-12T07:56:38Z"}],"article_type":"original","external_id":{"arxiv":["2404.15101"]},"OA_type":"gold","publication":"Communications Materials","date_created":"2024-08-11T22:01:11Z","OA_place":"publisher","title":"Designing athermal disordered solids with automatic differentiation","has_accepted_license":"1","month":"08","date_updated":"2025-05-08T09:45:35Z","fulldoi":"https://doi.org/10.1038/s43246-024-00583-4","file_date_updated":"2024-08-12T07:56:38Z","ddc":["530"],"language":[{"iso":"eng"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_processing_charge":"Yes","oa":1,"article_number":"141","scopus_import":"1","department":[{"_id":"CaGo"}],"publication_status":"published","publisher":"Springer Nature","publication_identifier":{"eissn":["2662-4443"]},"citation":{"ista":"Zu M, Goodrich CP. 2024. Designing athermal disordered solids with automatic differentiation. Communications Materials. 5, 141.","short":"M. Zu, C.P. Goodrich, Communications Materials 5 (2024).","ieee":"M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic differentiation,” Communications Materials, vol. 5. Springer Nature, 2024.","mla":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” Communications Materials, vol. 5, 141, Springer Nature, 2024, doi:10.1038/s43246-024-00583-4.","chicago":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” Communications Materials. Springer Nature, 2024. https://doi.org/10.1038/s43246-024-00583-4.","apa":"Zu, M., & Goodrich, C. P. (2024). Designing athermal disordered solids with automatic differentiation. Communications Materials. Springer Nature. https://doi.org/10.1038/s43246-024-00583-4","ama":"Zu M, Goodrich CP. Designing athermal disordered solids with automatic differentiation. Communications Materials. 2024;5. doi:10.1038/s43246-024-00583-4"},"intvolume":" 5","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","corr_author":"1","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"}],"volume":5,"quality_controlled":"1","doi":"10.1038/s43246-024-00583-4","APC_amount":"3534 EUR","acknowledgement":"We thank M. Lechner for helpful discussions.","_id":"17407","date_published":"2024-08-01T00:00:00Z","status":"public","year":"2024"},{"citation":{"ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4","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,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.","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.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4.","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.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023)."},"intvolume":" 14","publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"abstract":[{"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.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","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).","volume":14,"quality_controlled":"1","status":"public","year":"2023","_id":"14710","date_published":"2023-12-01T00:00:00Z","isi":1,"ddc":["530"],"pmid":1,"language":[{"iso":"eng"}],"oa":1,"article_number":"8328","scopus_import":"1","department":[{"_id":"CaGo"}],"article_processing_charge":"Yes","date_created":"2023-12-24T23:00:53Z","publication":"Nature Communications","title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","has_accepted_license":"1","month":"12","file_date_updated":"2023-12-27T08:40:43Z","date_updated":"2025-09-09T14:02:41Z","fulldoi":"https://doi.org/10.1038/s41467-023-43168-4","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","author":[{"full_name":"Curatolo, Agnese I.","first_name":"Agnese I.","last_name":"Curatolo"},{"full_name":"Kimchi, Ofer","last_name":"Kimchi","first_name":"Ofer"},{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Krueger, Ryan K.","last_name":"Krueger","first_name":"Ryan K."},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."}],"day":"01","article_type":"original","file":[{"file_id":"14714","content_type":"application/pdf","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","date_created":"2023-12-27T08:40:43Z","date_updated":"2023-12-27T08:40:43Z","file_name":"2023_NatureComm_Curatolo.pdf","file_size":1342319,"relation":"main_file","access_level":"open_access","creator":"kschuh","success":1}],"external_id":{"isi":["001125281300010"],"pmid":["38097568"]}},{"file_date_updated":"2022-03-10T12:10:25Z","fulldoi":"https://doi.org/10.15479/at:ista:10422","date_updated":"2026-04-08T06:58:55Z","month":"12","title":"Towards designer materials using customizable particle shape","has_accepted_license":"1","OA_place":"publisher","date_created":"2021-12-07T10:48:06Z","supervisor":[{"first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"}],"file":[{"date_created":"2021-12-07T11:13:52Z","checksum":"114e8f4b2c002c6c352416c12de2c695","content_type":"application/x-zip-compressed","file_id":"10424","creator":"cchlebak","relation":"source_file","access_level":"closed","date_updated":"2022-03-10T12:10:25Z","file_name":"Thesis.zip","file_size":394018},{"creator":"cchlebak","access_level":"closed","relation":"source_file","date_updated":"2022-03-10T12:10:25Z","file_name":"Preliminary_pages_Piankov.docx","file_size":47638,"date_created":"2021-12-07T11:14:01Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"cd15ae991ced352a9959815f794e657c","file_id":"10425"},{"file_size":484965,"date_updated":"2021-12-07T11:20:35Z","file_name":"2021_Piankov_combined.pdf","success":1,"creator":"cchlebak","access_level":"open_access","relation":"main_file","checksum":"e6899c798b75ba42fab9822bce309050","content_type":"application/pdf","file_id":"10426","date_created":"2021-12-07T11:20:35Z"}],"author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton","first_name":"Anton","last_name":"Piankov"}],"day":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","status":"public","year":"2021","_id":"10422","alternative_title":["ISTA Master's Thesis"],"date_published":"2021-12-07T00:00:00Z","doi":"10.15479/at:ista:10422","abstract":[{"text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","citation":{"ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10422.","mla":"Piankov, Anton. Towards Designer Materials Using Customizable Particle Shape. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10422.","apa":"Piankov, A. (2021). Towards designer materials using customizable particle shape. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10422","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:10.15479/at:ista:10422","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021."},"publication_status":"published","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2791-4585"]},"oa":1,"department":[{"_id":"GradSch"},{"_id":"CaGo"}],"article_processing_charge":"No","degree_awarded":"MS","language":[{"iso":"eng"}],"ddc":["530"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","author":[{"last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"King, Ella M.","first_name":"Ella M.","last_name":"King"},{"full_name":"Schoenholz, Samuel S.","last_name":"Schoenholz","first_name":"Samuel S."},{"full_name":"Cubuk, Ekin D.","first_name":"Ekin D.","last_name":"Cubuk"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"day":"09","article_type":"original","file":[{"file_name":"2021_PNAS_Goodrich.pdf","date_updated":"2021-03-22T12:23:54Z","file_size":1047954,"relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"9278","content_type":"application/pdf","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","date_created":"2021-03-22T12:23:54Z"}],"external_id":{"pmid":["33653960"],"isi":["000627429100097"]},"date_created":"2021-03-21T23:01:20Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","title":"Designing self-assembling kinetics with differentiable statistical physics models","issue":"10","month":"03","file_date_updated":"2021-03-22T12:23:54Z","date_updated":"2025-05-14T10:58:42Z","fulldoi":"https://doi.org/10.1073/pnas.2024083118","isi":1,"ddc":["530"],"pmid":1,"language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"CaGo"}],"article_number":"e2024083118","oa":1,"article_processing_charge":"No","intvolume":" 118","citation":{"ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 2021;118(10). doi:10.1073/pnas.2024083118","apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., & Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2024083118","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.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.","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,” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 10. National Academy of Sciences, 2021.","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.","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.","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)."},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","publisher":"National Academy of Sciences","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"}],"oa_version":"Published Version","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"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.","doi":"10.1073/pnas.2024083118","quality_controlled":"1","volume":118,"year":"2021","status":"public","date_published":"2021-03-09T00:00:00Z","_id":"9257"}]