[{"type":"journal_article","abstract":[{"lang":"eng","text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells."}],"intvolume":" 14","ddc":["530"],"title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14710","file":[{"success":1,"checksum":"fd9e9d527c2691f03fbc24031a75a3b3","date_created":"2023-12-27T08:40:43Z","date_updated":"2023-12-27T08:40:43Z","file_id":"14714","relation":"main_file","creator":"kschuh","file_size":1342319,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_NatureComm_Curatolo.pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","article_type":"original","citation":{"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.","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","ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. 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.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (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."},"publication":"Nature Communications","date_published":"2023-12-01T00:00:00Z","article_number":"8328","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-12-27T08:40:43Z","department":[{"_id":"CaGo"}],"publisher":"Springer Nature","publication_status":"published","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).","year":"2023","volume":14,"date_updated":"2024-01-02T11:36:46Z","date_created":"2023-12-24T23:00:53Z","author":[{"last_name":"Curatolo","first_name":"Agnese I.","full_name":"Curatolo, Agnese I."},{"last_name":"Kimchi","first_name":"Ofer","full_name":"Kimchi, Ofer"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Krueger, Ryan K.","last_name":"Krueger","first_name":"Ryan K."},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."}],"publication_identifier":{"eissn":["20411723"]},"month":"12","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-43168-4"},{"file_date_updated":"2023-02-23T10:42:07Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","article_number":"e2107588118","author":[{"full_name":"Li, Ling","first_name":"Ling","last_name":"Li"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Haizhao","last_name":"Yang","full_name":"Yang, Haizhao"},{"first_name":"Katherine R.","last_name":"Phillips","full_name":"Phillips, Katherine R."},{"first_name":"Zian","last_name":"Jia","full_name":"Jia, Zian"},{"last_name":"Chen","first_name":"Hongshun","full_name":"Chen, Hongshun"},{"full_name":"Wang, Lifeng","first_name":"Lifeng","last_name":"Wang"},{"last_name":"Zhong","first_name":"Jinjin","full_name":"Zhong, Jinjin"},{"first_name":"Anhua","last_name":"Liu","full_name":"Liu, Anhua"},{"full_name":"Lu, Jianfeng","first_name":"Jianfeng","last_name":"Lu"},{"first_name":"Jianwei","last_name":"Shuai","full_name":"Shuai, Jianwei"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."},{"full_name":"Spaepen, Frans","first_name":"Frans","last_name":"Spaepen"},{"first_name":"Joanna","last_name":"Aizenberg","full_name":"Aizenberg, Joanna"}],"volume":118,"date_created":"2023-02-21T08:51:04Z","date_updated":"2023-02-23T10:45:44Z","pmid":1,"year":"2021","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"08","doi":"10.1073/pnas.2107588118","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["34341109"]},"oa":1,"quality_controlled":"1","issue":"32","abstract":[{"lang":"eng","text":"Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"12674","checksum":"702f7ec60ce6f2815104ab649dc661a4","success":1,"date_updated":"2023-02-23T10:42:07Z","date_created":"2023-02-23T10:42:07Z","access_level":"open_access","file_name":"2021_PNAS_Li.pdf","content_type":"application/pdf","file_size":3275944,"creator":"dernst"}],"oa_version":"Published Version","_id":"12667","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 118","ddc":["570"],"status":"public","title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1","date_published":"2021-08-10T00:00:00Z","citation":{"ista":"Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 118(32), e2107588118.","ieee":"L. Li et al., “Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals,” PNAS, vol. 118, no. 32. Proceedings of the National Academy of Sciences, 2021.","apa":"Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg, J. (2021). Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2107588118","ama":"Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 2021;118(32). doi:10.1073/pnas.2107588118","chicago":"Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2107588118.","mla":"Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” PNAS, vol. 118, no. 32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2107588118.","short":"L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J. Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118 (2021)."},"publication":"PNAS","article_type":"original"},{"year":"2021","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.","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"CaGo"}],"author":[{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"King","first_name":"Ella M.","full_name":"King, Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","last_name":"Cubuk","full_name":"Cubuk, Ekin D."},{"full_name":"Brenner, Michael P.","first_name":"Michael P.","last_name":"Brenner"}],"date_updated":"2023-08-07T14:19:34Z","date_created":"2021-03-21T23:01:20Z","volume":118,"article_number":"e2024083118","file_date_updated":"2021-03-22T12:23:54Z","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2024083118","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"9257","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Designing self-assembling kinetics with differentiable statistical physics models","ddc":["530"],"intvolume":" 118","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9278","date_created":"2021-03-22T12:23:54Z","date_updated":"2021-03-22T12:23:54Z","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","success":1,"file_name":"2021_PNAS_Goodrich.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1047954,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"10","publication":"Proceedings of the National Academy of Sciences","citation":{"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. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2024083118.","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” Proceedings of the National Academy of Sciences, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:10.1073/pnas.2024083118.","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences 118 (2021).","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. 118(10), e2024083118.","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. National Academy of Sciences. 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, vol. 118, no. 10. National Academy of Sciences, 2021.","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. 2021;118(10). doi:10.1073/pnas.2024083118"},"article_type":"original","date_published":"2021-03-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1"},{"month":"12","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1126/sciadv.abc1939","language":[{"iso":"eng"}],"article_number":"eabc1939","file_date_updated":"2021-04-12T08:33:23Z","extern":"1","year":"2020","publication_status":"published","author":[{"last_name":"Kimchi","first_name":"Ofer","full_name":"Kimchi, Ofer"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Courbet, Alexis","first_name":"Alexis","last_name":"Courbet"},{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"full_name":"Woodall, Nicholas B.","first_name":"Nicholas B.","last_name":"Woodall"},{"full_name":"Baker, David","first_name":"David","last_name":"Baker"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"date_created":"2020-04-30T12:07:55Z","date_updated":"2021-04-12T08:35:19Z","volume":6,"day":"16","article_processing_charge":"No","has_accepted_license":"1","publication":"Science Advances","citation":{"ista":"Kimchi O, Goodrich CP, Courbet A, Curatolo AI, Woodall NB, Baker D, Brenner MP. 2020. Self-assembly-based posttranslational protein oscillators. Science Advances. 6(51), eabc1939.","apa":"Kimchi, O., Goodrich, C. P., Courbet, A., Curatolo, A. I., Woodall, N. B., Baker, D., & Brenner, M. P. (2020). Self-assembly-based posttranslational protein oscillators. Science Advances. https://doi.org/10.1126/sciadv.abc1939","ieee":"O. Kimchi et al., “Self-assembly-based posttranslational protein oscillators,” Science Advances, vol. 6, no. 51. 2020.","ama":"Kimchi O, Goodrich CP, Courbet A, et al. Self-assembly-based posttranslational protein oscillators. Science Advances. 2020;6(51). doi:10.1126/sciadv.abc1939","chicago":"Kimchi, Ofer, Carl Peter Goodrich, Alexis Courbet, Agnese I. Curatolo, Nicholas B. Woodall, David Baker, and Michael P. Brenner. “Self-Assembly-Based Posttranslational Protein Oscillators.” Science Advances, 2020. https://doi.org/10.1126/sciadv.abc1939.","mla":"Kimchi, Ofer, et al. “Self-Assembly-Based Posttranslational Protein Oscillators.” Science Advances, vol. 6, no. 51, eabc1939, 2020, doi:10.1126/sciadv.abc1939.","short":"O. Kimchi, C.P. Goodrich, A. Courbet, A.I. Curatolo, N.B. Woodall, D. Baker, M.P. Brenner, Science Advances 6 (2020)."},"article_type":"original","date_published":"2020-12-16T00:00:00Z","type":"journal_article","abstract":[{"text":"Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems.","lang":"eng"}],"issue":"51","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7778","title":"Self-assembly-based posttranslational protein oscillators","ddc":["570"],"status":"public","intvolume":" 6","file":[{"creator":"dernst","file_size":1259758,"content_type":"application/pdf","file_name":"2020_ScienceAdv_Kimchi.pdf","access_level":"open_access","date_updated":"2021-04-12T08:33:23Z","date_created":"2021-04-12T08:33:23Z","success":1,"checksum":"eb6d950b6a68ddc4a2fb31ec80a2a1bd","file_id":"9320","relation":"main_file"}],"oa_version":"Published Version"},{"intvolume":" 9","publisher":"Springer Nature","status":"public","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7754","year":"2018","volume":9,"oa_version":"Published Version","date_created":"2020-04-30T11:38:01Z","date_updated":"2021-01-12T08:15:18Z","author":[{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."},{"last_name":"Ribbeck","first_name":"Katharina","full_name":"Ribbeck, Katharina"}],"type":"journal_article","article_number":"4348","extern":"1","abstract":[{"lang":"eng","text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex."}],"quality_controlled":"1","article_type":"original","citation":{"ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","apa":"Goodrich, C. P., Brenner, M. P., & Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06851-5","ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” Nature Communications, vol. 9. Springer Nature, 2018.","ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 2018;9. doi:10.1038/s41467-018-06851-5","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06851-5.","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” Nature Communications, vol. 9, 4348, Springer Nature, 2018, doi:10.1038/s41467-018-06851-5.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018)."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-06851-5","open_access":"1"}],"publication":"Nature Communications","language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-06851-5","date_published":"2018-10-19T00:00:00Z","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","day":"19","month":"10"},{"publication_identifier":{"issn":["1531-7331","1545-4118"]},"article_processing_charge":"No","month":"07","day":"01","doi":"10.1146/annurev-matsci-070115-032036","date_published":"2017-07-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"ama":"Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 2017;47:217-246. doi:10.1146/annurev-matsci-070115-032036","ista":"Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.","apa":"Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. Annual Reviews. https://doi.org/10.1146/annurev-matsci-070115-032036","ieee":"J. P. Sethna et al., “Deformation of crystals: Connections with statistical physics,” Annual Review of Materials Research, vol. 47. Annual Reviews, pp. 217–246, 2017.","mla":"Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:10.1146/annurev-matsci-070115-032036.","short":"J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246.","chicago":"Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” Annual Review of Materials Research. Annual Reviews, 2017. https://doi.org/10.1146/annurev-matsci-070115-032036."},"main_file_link":[{"url":"https://doi.org/10.1146/annurev-matsci-070115-032036","open_access":"1"}],"publication":"Annual Review of Materials Research","page":"217-246","quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales."}],"extern":"1","type":"journal_article","author":[{"first_name":"James P.","last_name":"Sethna","full_name":"Sethna, James P."},{"full_name":"Bierbaum, Matthew K.","last_name":"Bierbaum","first_name":"Matthew K."},{"full_name":"Dahmen, Karin A.","last_name":"Dahmen","first_name":"Karin A."},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"first_name":"Julia R.","last_name":"Greer","full_name":"Greer, Julia R."},{"first_name":"Lorien X.","last_name":"Hayden","full_name":"Hayden, Lorien X."},{"last_name":"Kent-Dobias","first_name":"Jaron P.","full_name":"Kent-Dobias, Jaron P."},{"last_name":"Lee","first_name":"Edward D.","full_name":"Lee, Edward D."},{"full_name":"Liarte, Danilo B.","first_name":"Danilo B.","last_name":"Liarte"},{"full_name":"Ni, Xiaoyue","last_name":"Ni","first_name":"Xiaoyue"},{"full_name":"Quinn, Katherine N.","first_name":"Katherine N.","last_name":"Quinn"},{"full_name":"Raju, Archishman","first_name":"Archishman","last_name":"Raju"},{"full_name":"Rocklin, D. Zeb","last_name":"Rocklin","first_name":"D. Zeb"},{"first_name":"Ashivni","last_name":"Shekhawat","full_name":"Shekhawat, Ashivni"},{"full_name":"Zapperi, Stefano","last_name":"Zapperi","first_name":"Stefano"}],"oa_version":"Published Version","volume":47,"date_created":"2020-04-30T11:38:24Z","date_updated":"2021-01-12T08:15:18Z","_id":"7755","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Annual Reviews","intvolume":" 47","status":"public","title":"Deformation of crystals: Connections with statistical physics","publication_status":"published"},{"author":[{"first_name":"Jason W.","last_name":"Rocks","full_name":"Rocks, Jason W."},{"full_name":"Pashine, Nidhi","first_name":"Nidhi","last_name":"Pashine"},{"full_name":"Bischofberger, Irmgard","last_name":"Bischofberger","first_name":"Irmgard"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"date_created":"2020-04-30T11:38:53Z","date_updated":"2021-01-12T08:15:19Z","volume":114,"oa_version":"None","year":"2017","_id":"7757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Designing allostery-inspired response in mechanical networks","status":"public","publication_status":"published","intvolume":" 114","publisher":"Proceedings of the National Academy of Sciences","abstract":[{"text":"Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks.","lang":"eng"}],"issue":"10","extern":"1","type":"journal_article","doi":"10.1073/pnas.1612139114","date_published":"2017-03-07T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1612139114.","mla":"Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” Proceedings of the National Academy of Sciences, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:10.1073/pnas.1612139114.","short":"J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.","ista":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525.","ieee":"J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” Proceedings of the National Academy of Sciences, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017.","apa":"Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612139114","ama":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 2017;114(10):2520-2525. doi:10.1073/pnas.1612139114"},"article_type":"original","quality_controlled":"1","page":"2520-2525","month":"03","day":"07","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424","1091-6490"]}},{"type":"journal_article","extern":"1","issue":"2","abstract":[{"text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.","lang":"eng"}],"publisher":"Proceedings of the National Academy of Sciences","intvolume":" 114","status":"public","title":"Using active colloids as machines to weave and braid on the micrometer scale","publication_status":"published","_id":"7758","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":114,"oa_version":"None","date_created":"2020-04-30T11:39:09Z","date_updated":"2021-01-12T08:15:20Z","author":[{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"article_processing_charge":"No","publication_identifier":{"issn":["0027-8424","1091-6490"]},"day":"10","month":"01","page":"257-262","quality_controlled":"1","article_type":"original","citation":{"short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262.","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:10.1073/pnas.1608838114.","chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1608838114.","ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 2017;114(2):257-262. doi:10.1073/pnas.1608838114","apa":"Goodrich, C. P., & Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1608838114","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” Proceedings of the National Academy of Sciences, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262."},"publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"date_published":"2017-01-10T00:00:00Z","doi":"10.1073/pnas.1608838114"},{"type":"journal_article","extern":"1","issue":"3-4","abstract":[{"lang":"eng","text":"We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor."}],"intvolume":" 167","publisher":"Springer Nature","publication_status":"published","status":"public","title":"Emergent SO(3) symmetry of the frictionless shear jamming transition","_id":"7756","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":167,"date_created":"2020-04-30T11:38:38Z","date_updated":"2021-01-12T08:15:19Z","author":[{"first_name":"Marco","last_name":"Baity-Jesi","full_name":"Baity-Jesi, Marco"},{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."},{"first_name":"James P.","last_name":"Sethna","full_name":"Sethna, James P."}],"article_processing_charge":"No","publication_identifier":{"issn":["0022-4715","1572-9613"]},"day":"03","month":"01","page":"735-748","article_type":"original","quality_controlled":"1","citation":{"ama":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 2017;167(3-4):735-748. doi:10.1007/s10955-016-1703-9","ista":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748.","ieee":"M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.","apa":"Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., & Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-016-1703-9","mla":"Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:10.1007/s10955-016-1703-9.","short":"M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748.","chicago":"Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” Journal of Statistical Physics. Springer Nature, 2017. https://doi.org/10.1007/s10955-016-1703-9."},"publication":"Journal of Statistical Physics","language":[{"iso":"eng"}],"date_published":"2017-01-03T00:00:00Z","doi":"10.1007/s10955-016-1703-9"},{"publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No","month":"02","day":"23","citation":{"short":"J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters 116 (2016).","mla":"Rieser, Jennifer M., et al. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” Physical Review Letters, vol. 116, no. 8, 088001, American Physical Society, 2016, doi:10.1103/physrevlett.116.088001.","chicago":"Rieser, Jennifer M., Carl Peter Goodrich, Andrea J. Liu, and Douglas J. Durian. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.116.088001.","ama":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. 2016;116(8). doi:10.1103/physrevlett.116.088001","ieee":"J. M. Rieser, C. P. Goodrich, A. J. Liu, and D. J. Durian, “Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials,” Physical Review Letters, vol. 116, no. 8. American Physical Society, 2016.","apa":"Rieser, J. M., Goodrich, C. P., Liu, A. J., & Durian, D. J. (2016). Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.116.088001","ista":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. 2016. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. 116(8), 088001."},"publication":"Physical Review Letters","quality_controlled":"1","article_type":"original","doi":"10.1103/physrevlett.116.088001","date_published":"2016-02-23T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","article_number":"088001 ","issue":"8","abstract":[{"lang":"eng","text":"Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7762","year":"2016","intvolume":" 116","publisher":"American Physical Society","title":"Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials","status":"public","publication_status":"published","author":[{"first_name":"Jennifer M.","last_name":"Rieser","full_name":"Rieser, Jennifer M."},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"last_name":"Durian","first_name":"Douglas J.","full_name":"Durian, Douglas J."}],"oa_version":"None","volume":116,"date_updated":"2021-01-12T08:15:22Z","date_created":"2020-04-30T11:40:25Z"},{"publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No","month":"06","day":"10","citation":{"chicago":"Graves, Amy L., Samer Nashed, Elliot Padgett, Carl Peter Goodrich, Andrea J. Liu, and James P. Sethna. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.116.235501.","short":"A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna, Physical Review Letters 116 (2016).","mla":"Graves, Amy L., et al. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” Physical Review Letters, vol. 116, no. 23, 235501, American Physical Society, 2016, doi:10.1103/physrevlett.116.235501.","ieee":"A. L. Graves, S. Nashed, E. Padgett, C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Pinning susceptibility: The effect of dilute, quenched disorder on jamming,” Physical Review Letters, vol. 116, no. 23. American Physical Society, 2016.","apa":"Graves, A. L., Nashed, S., Padgett, E., Goodrich, C. P., Liu, A. J., & Sethna, J. P. (2016). Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.116.235501","ista":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. 2016. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. 116(23), 235501.","ama":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. 2016;116(23). doi:10.1103/physrevlett.116.235501"},"publication":"Physical Review Letters","quality_controlled":"1","article_type":"original","date_published":"2016-06-10T00:00:00Z","doi":"10.1103/physrevlett.116.235501","language":[{"iso":"eng"}],"type":"journal_article","article_number":"235501","issue":"23","abstract":[{"text":"We study the effect of dilute pinning on the jamming transition. Pinning reduces the average contact number needed to jam unpinned particles and shifts the jamming threshold to lower densities, leading to a pinning susceptibility, χp. Our main results are that this susceptibility obeys scaling form and diverges in the thermodynamic limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins. Finite-size scaling arguments yield these values with associated statistical (systematic) errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic corrections raise the exponent in d=2 to close to the d=3 value, although the systematic errors are very large.","lang":"eng"}],"extern":"1","_id":"7761","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","intvolume":" 116","publisher":"American Physical Society","title":"Pinning susceptibility: The effect of dilute, quenched disorder on jamming","status":"public","publication_status":"published","author":[{"last_name":"Graves","first_name":"Amy L.","full_name":"Graves, Amy L."},{"full_name":"Nashed, Samer","last_name":"Nashed","first_name":"Samer"},{"full_name":"Padgett, Elliot","first_name":"Elliot","last_name":"Padgett"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Sethna, James P.","first_name":"James P.","last_name":"Sethna"}],"volume":116,"oa_version":"None","date_updated":"2021-01-12T08:15:21Z","date_created":"2020-04-30T11:40:10Z"},{"month":"03","day":"14","article_processing_charge":"No","publication_identifier":{"issn":["1744-683X","1744-6848"]},"publication":"Soft Matter","citation":{"ista":"Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self stress in jammed systems. Soft Matter. 12(17), 3982–3990.","ieee":"D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states of self stress in jammed systems,” Soft Matter, vol. 12, no. 17. Royal Society of Chemistry, pp. 3982–3990, 2016.","apa":"Sussman, D. M., Goodrich, C. P., & Liu, A. J. (2016). Spatial structure of states of self stress in jammed systems. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm00094k","ama":"Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress in jammed systems. Soft Matter. 2016;12(17):3982-3990. doi:10.1039/c6sm00094k","chicago":"Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure of States of Self Stress in Jammed Systems.” Soft Matter. Royal Society of Chemistry, 2016. https://doi.org/10.1039/c6sm00094k.","mla":"Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed Systems.” Soft Matter, vol. 12, no. 17, Royal Society of Chemistry, 2016, pp. 3982–90, doi:10.1039/c6sm00094k.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990."},"quality_controlled":"1","article_type":"original","page":"3982-3990","date_published":"2016-03-14T00:00:00Z","doi":"10.1039/c6sm00094k","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"States of self stress, organizations of internal forces in many-body systems that are in equilibrium with an absence of external forces, can be thought of as the constitutive building blocks of the elastic response of a material. In overconstrained disordered packings they have a natural mathematical correspondence with the zero-energy vibrational modes in underconstrained systems. While substantial attention in the literature has been paid to diverging length scales associated with zero- and finite-energy vibrational modes in jammed systems, less is known about the spatial structure of the states of self stress. In this work we define a natural way in which a unique state of self stress can be associated with each bond in a disordered spring network derived from a jammed packing, and then investigate the spatial structure of these bond-localized states of self stress. This allows for an understanding of how the elastic properties of a system would change upon changing the strength or even existence of any bond in the system."}],"issue":"17","extern":"1","_id":"7764","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Spatial structure of states of self stress in jammed systems","intvolume":" 12","publisher":"Royal Society of Chemistry","author":[{"first_name":"Daniel M.","last_name":"Sussman","full_name":"Sussman, Daniel M."},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"}],"related_material":{"link":[{"relation":"other","url":"https://doi.org/10.1039/c6sm02496c"}]},"date_created":"2020-04-30T11:40:56Z","date_updated":"2021-01-12T08:15:22Z","oa_version":"None","volume":12},{"month":"01","day":"15","publication_identifier":{"issn":["0021-9991"]},"article_processing_charge":"No","publication":"Journal of Computational Physics","citation":{"ieee":"R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B. R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena,” Journal of Computational Physics, vol. 305. Elsevier, pp. 244–262, 2016.","apa":"Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., & Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. Elsevier. https://doi.org/10.1016/j.jcp.2015.10.035","ista":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. 305, 244–262.","ama":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. 2016;305:244-262. doi:10.1016/j.jcp.2015.10.035","chicago":"Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys, Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” Journal of Computational Physics. Elsevier, 2016. https://doi.org/10.1016/j.jcp.2015.10.035.","short":"R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson, Journal of Computational Physics 305 (2016) 244–262.","mla":"Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” Journal of Computational Physics, vol. 305, Elsevier, 2016, pp. 244–62, doi:10.1016/j.jcp.2015.10.035."},"quality_controlled":"1","article_type":"original","page":"244-262","doi":"10.1016/j.jcp.2015.10.035","date_published":"2016-01-15T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"An orthogonal wavelet basis is characterized by its approximation order, which relates to the ability of the basis to represent general smooth functions on a given scale. It is known, though perhaps not widely known, that there are ways of exceeding the approximation order, i.e., achieving higher-order error in the discretized wavelet transform and its inverse. The focus here is on the development of a practical formulation to accomplish this first for 1D smooth functions, then for 1D functions with discontinuities and then for multidimensional (here 2D) functions with discontinuities. It is shown how to transcend both the wavelet approximation order and the 2D Gibbs phenomenon in representing electromagnetic fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis grid.","lang":"eng"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7763","year":"2016","status":"public","publication_status":"published","title":"Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena","intvolume":" 305","publisher":"Elsevier","author":[{"first_name":"Richard","last_name":"Lombardini","full_name":"Lombardini, Richard"},{"full_name":"Acevedo, Ramiro","first_name":"Ramiro","last_name":"Acevedo"},{"full_name":"Kuczala, Alexander","last_name":"Kuczala","first_name":"Alexander"},{"last_name":"Keys","first_name":"Kerry P.","full_name":"Keys, Kerry P."},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Johnson, Bruce R.","last_name":"Johnson","first_name":"Bruce R."}],"date_updated":"2021-01-12T08:15:22Z","date_created":"2020-04-30T11:40:41Z","oa_version":"None","volume":305},{"author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"James P.","last_name":"Sethna","full_name":"Sethna, James P."}],"date_updated":"2021-01-12T08:15:21Z","date_created":"2020-04-30T11:39:53Z","oa_version":"None","volume":113,"_id":"7760","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Scaling ansatz for the jamming transition","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","intvolume":" 113","abstract":[{"lang":"eng","text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming."}],"issue":"35","extern":"1","type":"journal_article","doi":"10.1073/pnas.1601858113","date_published":"2016-08-30T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 2016;113(35):9745-9750. doi:10.1073/pnas.1601858113","apa":"Goodrich, C. P., Liu, A. J., & Sethna, J. P. (2016). Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1601858113","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” Proceedings of the National Academy of Sciences, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750.","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” Proceedings of the National Academy of Sciences, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:10.1073/pnas.1601858113.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1601858113."},"article_type":"original","quality_controlled":"1","page":"9745-9750","day":"30","month":"08","publication_identifier":{"issn":["0027-8424","1091-6490"]},"article_processing_charge":"No"},{"year":"2015","_id":"7765","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","publication_status":"published","status":"public","intvolume":" 114","publisher":"American Physical Society","author":[{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"date_created":"2020-04-30T11:41:08Z","date_updated":"2021-01-12T08:15:23Z","volume":114,"oa_version":"None","article_number":"225501","type":"journal_article","abstract":[{"lang":"eng","text":"We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior."}],"issue":"22","extern":"1","publication":"Physical Review Letters","citation":{"ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.","ista":"Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501."},"article_type":"original","quality_controlled":"1","date_published":"2015-06-04T00:00:00Z","doi":"10.1103/physrevlett.114.225501","language":[{"iso":"eng"}],"day":"04","month":"06","publication_identifier":{"issn":["0031-9007","1079-7114"]},"article_processing_charge":"No"},{"extern":"1","abstract":[{"lang":"eng","text":"We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food."}],"issue":"3","article_number":"032706","type":"journal_article","date_created":"2020-04-30T11:41:38Z","date_updated":"2021-01-12T08:15:24Z","volume":91,"oa_version":"None","author":[{"last_name":"van Drongelen","first_name":"Ruben","full_name":"van Drongelen, Ruben"},{"full_name":"Pal, Anshuman","last_name":"Pal","first_name":"Anshuman"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"}],"publication_status":"published","title":"Collective dynamics of soft active particles","status":"public","publisher":"American Physical Society","intvolume":" 91","year":"2015","_id":"7767","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","day":"01","publication_identifier":{"issn":["1539-3755","1550-2376"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1103/physreve.91.032706","date_published":"2015-03-01T00:00:00Z","quality_controlled":"1","article_type":"original","publication":"Physical Review E","citation":{"chicago":"Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","mla":"van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706.","apa":"van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706","ieee":"R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015.","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","ama":"van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706"}},{"_id":"7766","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","publisher":"Royal Society of Chemistry","intvolume":" 11","title":"Disordered surface vibrations in jammed sphere packings","status":"public","publication_status":"published","author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"volume":11,"oa_version":"None","date_created":"2020-04-30T11:41:23Z","date_updated":"2021-01-12T08:15:23Z","type":"journal_article","issue":"14","abstract":[{"lang":"eng","text":"We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached."}],"extern":"1","citation":{"mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015."},"publication":"Soft Matter","page":"2745-2751","quality_controlled":"1","article_type":"original","date_published":"2015-02-15T00:00:00Z","doi":"10.1039/c4sm02905d","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1744-683X","1744-6848"]},"month":"02","day":"15"},{"article_processing_charge":"No","day":"29","month":"10","page":"242","external_id":{"arxiv":["1510.08820"]},"oa":1,"citation":{"chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","short":"C.P. Goodrich, ArXiv:1510.08820 (2015).","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.","apa":"Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820.","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv:1510.08820. 2015.","ista":"Goodrich CP. 2015. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:1510.08820, .","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv:151008820. 2015."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.08820"}],"publication":"arXiv:1510.08820","language":[{"iso":"eng"}],"date_published":"2015-10-29T00:00:00Z","type":"preprint","extern":"1","abstract":[{"lang":"eng","text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties."}],"status":"public","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","publication_status":"published","_id":"7779","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","oa_version":"Preprint","date_updated":"2021-01-12T08:15:28Z","date_created":"2020-04-30T12:16:18Z","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"}]},{"publication_identifier":{"issn":["1539-3755","1550-2376"]},"article_processing_charge":"No","month":"12","day":"05","citation":{"mla":"Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical Review E, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:10.1103/physreve.90.062305.","short":"M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz, C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).","chicago":"Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson, Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.90.062305.","ama":"Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 2014;90(6). doi:10.1103/physreve.90.062305","ista":"Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 90(6), 062305.","apa":"Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz, K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.062305","ieee":"M. A. Lohr et al., “Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings,” Physical Review E, vol. 90, no. 6. American Physical Society, 2014."},"publication":"Physical Review E","article_type":"original","quality_controlled":"1","doi":"10.1103/physreve.90.062305","date_published":"2014-12-05T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","article_number":"062305","issue":"6","abstract":[{"text":"We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material.","lang":"eng"}],"extern":"1","year":"2014","_id":"7768","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","intvolume":" 90","publication_status":"published","title":"Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings","status":"public","author":[{"first_name":"Matthew A.","last_name":"Lohr","full_name":"Lohr, Matthew A."},{"last_name":"Still","first_name":"Tim","full_name":"Still, Tim"},{"last_name":"Ganti","first_name":"Raman","full_name":"Ganti, Raman"},{"first_name":"Matthew D.","last_name":"Gratale","full_name":"Gratale, Matthew D."},{"last_name":"Davidson","first_name":"Zoey S.","full_name":"Davidson, Zoey S."},{"full_name":"Aptowicz, Kevin B.","last_name":"Aptowicz","first_name":"Kevin B."},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Sussman","first_name":"Daniel M.","full_name":"Sussman, Daniel M."},{"full_name":"Yodh, A. G.","last_name":"Yodh","first_name":"A. G."}],"oa_version":"None","volume":90,"date_created":"2020-04-30T11:41:54Z","date_updated":"2021-01-12T08:15:24Z"},{"publication_status":"published","publisher":"American Physical Society","year":"2014","date_updated":"2021-01-12T08:15:26Z","date_created":"2020-04-30T11:42:39Z","volume":112,"author":[{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"article_number":"049801 ","extern":"1","external_id":{"arxiv":["1306.1285"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.1285"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.112.049801","month":"04","publication_identifier":{"issn":["0031-9007","1079-7114"]},"title":"Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”","status":"public","intvolume":" 112","_id":"7771","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is \"no harmonic regime in the large system limit for all compressions\" and \"at jamming onset for any system size.\" Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. "}],"issue":"4","article_type":"letter_note","publication":"Physical Review Letters","citation":{"mla":"Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters, vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801.","ama":"Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” Physical Review Letters. 2014;112(4). doi:10.1103/physrevlett.112.049801","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”. Physical Review Letters. 112(4), 049801.","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact interactions make jammed particulate systems inherently nonharmonic,’” Physical Review Letters, vol. 112, no. 4. American Physical Society, 2014.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801"},"date_published":"2014-04-20T00:00:00Z","day":"20","article_processing_charge":"No"}]