The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.
Designing allostery-inspired response in mechanical networks
Open accessAbstract
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.
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“Optimizing the networks for a geometric task, by selecting network structures where binding a ligand leads to a defined displacement on the other side of the network (“active site”), yields networks displaying a powerful lever at the active site, where the signal is required (Flechsig, 2017; Rocks et al., 2017; Yan et al., 2017a, 2017b).”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Rocks et al., 2017
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Citations
Cites
Jamming at zero temperature and zero applied stress: The epitome of disorder
O’Hern, C. S., Silbert, L. E., Liu, A. J., & Nagel, S. R. (2003) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.68.011306 · Cited by 1,604 · cited 1×
“Our networks are generated from random configurations of soft spheres in three dimensions or disks in two dimensions with periodic boundary conditions that have been brought to a local energy minimum using standard jamming algorithms (5, 6); the spheres overlap and are in mechanical equilibrium.”
MethodAdjustment of an Inverse Matrix Corresponding to a Change in One Element of a Given Matrix
Sherman, J., & Morrison, W. J. (1950) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177729893 · Cited by 1,402 · cited 2×
“The total energy can then be written as E = 1 2 〈u|H|u〉, [4] where the Hessian matrix H = QF−1QT is a dN× dN matrix.”
MethodThe ensemble nature of allostery
Motlagh, H. N., Wrabl, J. O., Li, J., & Hilser, V. J. (2014) · Nature · doi:10.1038/nature13001 · Cited by 1,247 · cited 1×
“Statistical fluctuations in the structure of proteins have been shown to play an important role in allosteric functionality (22, 23).”
BackgroundIs allostery an intrinsic property of all dynamic proteins?
Gunasekaran, K., Ma, B., & Nussinov, R. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20232 · Cited by 896 · cited 1×
“This finding can be viewed as a first step towards understanding why allosteric behavior is so common in biopolymers [5].”
BackgroundThe Jamming Transition and the Marginally Jammed Solid
Liu, A. J., & Nagel, S. R. (2010) · Annual Review of Condensed Matter Physics · doi:10.1146/annurev-conmatphys-070909-104045 · Cited by 860 · cited 1×
“Our networks are generated from random configurations of soft spheres in three dimensions or disks in two dimensions with periodic boundary conditions that have been brought to a local energy minimum using standard jamming algorithms (5, 6); the spheres overlap and are in mechanical equilibrium.”
MethodAllostery in Disease and in Drug Discovery
Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769
Calladine, C. R. (1978) · International Journal of Solids and Structures · doi:10.1016/0020-7683(78)90052-5 · Cited by 657 · cited 3×
“By Maxwell-Calladine counting, N0 − Ns = dN − Nb, where N0 is the number of zero modes [13].”
BackgroundInfluentialGlobal dynamics of proteins: bridging between structure and function
Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131258 · Cited by 610 · cited 1×
“In fact, folded proteins have long been modeled as elastic networks (13), and the response to localized forces in the resulting networks has been studied (14).”
BackgroundProtein promiscuity and its implications for biotechnology
Nobeli, I., Favia, A. D., & Thornton, J. M. (2009) · Nature Biotechnology · doi:10.1038/nbt1519 · Cited by 508
Allostery: Absence of a change in shape does not imply that allostery is not at play
Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.02.034 · Cited by 453 · cited 1×
“Statistical fluctuations in the structure of proteins have been shown to play an important role in allosteric functionality (22, 23).”
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New frontiers for the materials genome initiative
Pablo, J., Jackson, N. E., Webb, M. A., Chen, L., Moore, J. E., Morgan, D. D., Jacobs, R. M., Pollock, T. M., Schlom, D. G., Toberer, E. S., et al. (2019) · npj Computational Materials · doi:10.1038/s41524-019-0173-4 · Cited by 594
“167,168 Other examples have shown that it is possible to print 2D structures that subsequently fold along specific pathways to form elaborate 3D objects.”
Allostery in Its Many Disguises: From Theory to Applications
Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404
Deep Learning in Mechanical Metamaterials: From Prediction and Generation to Inverse Design
Zheng, X., Zhang, X., Chen, T., & Watanabe, I. (2023) · Advanced Materials · doi:10.1002/adma.202302530 · Cited by 407
Yasuda, H., Buskohl, P. R., Gillman, A. S., Murphey, T. D., Stepney, S., Vaia, R. A., & Raney, J. R. (2021) · Nature · doi:10.1038/s41586-021-03623-y · Cited by 320
Network analysis of particles and grains
Papadopoulos, L., Porter, M. A., Daniels, K. E., & Bassett, D. S. (2018) · Journal of Complex Networks · doi:10.1093/comnet/cny005 · Cited by 216
“Motivated by allosteric responses in proteins, [382] developed an approach that allows careful control of local mechanical responses in”
Background
Metadata
- Authors
- Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R.
- Affiliations
- University of Pennsylvania (US)
- University of Chicago (US)
- Massachusetts Institute of Technology (US)
- Harvard University (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2017-02-21
- Volume
- 114
- Issue
- 10
- Pages
- 2520-2525
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC5347623
- OpenAlex
- W2485975781
- Cited by
- 204
- References
- 33
- Citations by year
- 2026: 17 · 2025: 34 · 2024: 18 · 2023: 22 · 2022: 12 · 2021: 27 · 2020: 22 · 2019: 29 · 2018: 14 · 2017: 8
- FWCI
- 15.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- arXiv (Cornell University)
- Funders
- U.S. Department of Energy (DE-FG02-05ER46199, DE-FG02-03ER46088)
- National Science Foundation Graduate Research Fellowship Program (DGE-1321851)
- Simons Foundation (305547, 327939)
- DOC | National Institute of Standards and Technology (60NANB15D055)
- Topics
- Physical Sciences › Engineering › Mechanical Engineering › Advanced Materials and Mechanics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular Mechanics and Interactions
- Physical Sciences › Physics and Astronomy › Acoustics and Ultrasonics › Acoustic Wave Phenomena Research
- Keywords
- allosteric regulation, mechanical metamaterials, spring networks, strain amplification, disordered networks, protein conformational change, network design
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