---
_id: '14710'
abstract:
- lang: eng
text: The self-assembly of complex structures from a set of non-identical building
blocks is a hallmark of soft matter and biological systems, including protein
complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence
of the equilibrium assembly yield on the concentrations and interaction energies
of building blocks is highly challenging, owing to the difficulty of computing
the entropic contributions to the free energy of the many structures that compete
with the ground state configuration. While these calculations yield well known
results for spherically symmetric building blocks, they do not hold when the building
blocks have internal rotational degrees of freedom. Here we present an approach
for solving this problem that works with arbitrary building blocks, including
proteins with known structure and complex colloidal building blocks. Our algorithm
combines classical statistical mechanics with recently developed computational
tools for automatic differentiation. Automatic differentiation allows efficient
evaluation of equilibrium averages over configurations that would otherwise be
intractable. We demonstrate the validity of our framework by comparison to molecular
dynamics simulations of simple examples, and apply it to calculate the yield curves
for known protein complexes and for the assembly of colloidal shells.
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).'
article_number: '8328'
article_processing_charge: Yes
article_type: original
author:
- first_name: Agnese I.
full_name: Curatolo, Agnese I.
last_name: Curatolo
- first_name: Ofer
full_name: Kimchi, Ofer
last_name: Kimchi
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ryan K.
full_name: Krueger, Ryan K.
last_name: Krueger
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
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
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.
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.
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.
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.
short: A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature
Communications 14 (2023).
date_created: 2023-12-24T23:00:53Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-02T11:36:46Z
day: '01'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1038/s41467-023-43168-4
file:
- access_level: open_access
checksum: fd9e9d527c2691f03fbc24031a75a3b3
content_type: application/pdf
creator: kschuh
date_created: 2023-12-27T08:40:43Z
date_updated: 2023-12-27T08:40:43Z
file_id: '14714'
file_name: 2023_NatureComm_Curatolo.pdf
file_size: 1342319
relation: main_file
success: 1
file_date_updated: 2023-12-27T08:40:43Z
has_accepted_license: '1'
intvolume: ' 14'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A computational toolbox for the assembly yield of complex and heterogeneous
structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '9257'
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.'
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.
article_number: e2024083118
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ella M.
full_name: King, Ella M.
last_name: King
- first_name: Samuel S.
full_name: Schoenholz, Samuel S.
last_name: Schoenholz
- first_name: Ekin D.
full_name: Cubuk, Ekin D.
last_name: Cubuk
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
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. 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. 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.
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, vol. 118, no. 10. National
Academy of Sciences, 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.
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).
date_created: 2021-03-21T23:01:20Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2023-08-07T14:19:34Z
day: '09'
ddc:
- '530'
department:
- _id: CaGo
doi: 10.1073/pnas.2024083118
external_id:
isi:
- '000627429100097'
pmid:
- '33653960'
file:
- access_level: open_access
checksum: 5be8da2b1c0757feb1057f1a515cf9e0
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T12:23:54Z
date_updated: 2021-03-22T12:23:54Z
file_id: '9278'
file_name: 2021_PNAS_Goodrich.pdf
file_size: 1047954
relation: main_file
success: 1
file_date_updated: 2021-03-22T12:23:54Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing self-assembling kinetics with differentiable statistical physics
models
tmp:
image: /images/cc_by_nc_nd.png
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)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 118
year: '2021'
...
---
_id: '12667'
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.
article_number: e2107588118
article_processing_charge: No
article_type: original
author:
- first_name: Ling
full_name: Li, Ling
last_name: Li
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Haizhao
full_name: Yang, Haizhao
last_name: Yang
- first_name: Katherine R.
full_name: Phillips, Katherine R.
last_name: Phillips
- first_name: Zian
full_name: Jia, Zian
last_name: Jia
- first_name: Hongshun
full_name: Chen, Hongshun
last_name: Chen
- first_name: Lifeng
full_name: Wang, Lifeng
last_name: Wang
- first_name: Jinjin
full_name: Zhong, Jinjin
last_name: Zhong
- first_name: Anhua
full_name: Liu, Anhua
last_name: Liu
- first_name: Jianfeng
full_name: Lu, Jianfeng
last_name: Lu
- first_name: Jianwei
full_name: Shuai, Jianwei
last_name: Shuai
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
- first_name: Frans
full_name: Spaepen, Frans
last_name: Spaepen
- first_name: Joanna
full_name: Aizenberg, Joanna
last_name: Aizenberg
citation:
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
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
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.
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.
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.
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).
date_created: 2023-02-21T08:51:04Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-02-23T10:45:44Z
day: '10'
ddc:
- '570'
doi: 10.1073/pnas.2107588118
extern: '1'
external_id:
pmid:
- '34341109'
file:
- access_level: open_access
checksum: 702f7ec60ce6f2815104ab649dc661a4
content_type: application/pdf
creator: dernst
date_created: 2023-02-23T10:42:07Z
date_updated: 2023-02-23T10:42:07Z
file_id: '12674'
file_name: 2021_PNAS_Li.pdf
file_size: 3275944
relation: main_file
success: 1
file_date_updated: 2023-02-23T10:42:07Z
has_accepted_license: '1'
intvolume: ' 118'
issue: '32'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: PNAS
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Microscopic origins of the crystallographically preferred growth in evaporation-induced
colloidal crystals
tmp:
image: /images/cc_by_nc_nd.png
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)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2021'
...
---
_id: '7778'
abstract:
- lang: eng
text: Recent advances in synthetic posttranslational protein circuits are substantially
impacting the landscape of cellular engineering and offer several advantages compared
to traditional gene circuits. However, engineering dynamic phenomena such as oscillations
in protein-level circuits remains an outstanding challenge. Few examples of biological
posttranslational oscillators are known, necessitating theoretical progress to
determine realizable oscillators. We construct mathematical models for two posttranslational
oscillators, using few components that interact only through reversible binding
and phosphorylation/dephosphorylation reactions. Our designed oscillators rely
on the self-assembly of two protein species into multimeric functional enzymes
that respectively inhibit and enhance this self-assembly. We limit our analysis
to within experimental constraints, finding (i) significant portions of the restricted
parameter space yielding oscillations and (ii) that oscillation periods can be
tuned by several orders of magnitude using recent advances in computational protein
design. Our work paves the way for the rational design and realization of protein-based
dynamic systems.
article_number: eabc1939
article_processing_charge: No
article_type: original
author:
- first_name: Ofer
full_name: Kimchi, Ofer
last_name: Kimchi
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Alexis
full_name: Courbet, Alexis
last_name: Courbet
- first_name: Agnese I.
full_name: Curatolo, Agnese I.
last_name: Curatolo
- first_name: Nicholas B.
full_name: Woodall, Nicholas B.
last_name: Woodall
- first_name: David
full_name: Baker, David
last_name: Baker
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
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
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
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.
ieee: O. Kimchi et al., “Self-assembly-based posttranslational protein oscillators,”
Science Advances, vol. 6, no. 51. 2020.
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.
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).
date_created: 2020-04-30T12:07:55Z
date_published: 2020-12-16T00:00:00Z
date_updated: 2021-04-12T08:35:19Z
day: '16'
ddc:
- '570'
doi: 10.1126/sciadv.abc1939
extern: '1'
file:
- access_level: open_access
checksum: eb6d950b6a68ddc4a2fb31ec80a2a1bd
content_type: application/pdf
creator: dernst
date_created: 2021-04-12T08:33:23Z
date_updated: 2021-04-12T08:33:23Z
file_id: '9320'
file_name: 2020_ScienceAdv_Kimchi.pdf
file_size: 1259758
relation: main_file
success: 1
file_date_updated: 2021-04-12T08:33:23Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '51'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_status: published
quality_controlled: '1'
status: public
title: Self-assembly-based posttranslational protein oscillators
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2020'
...
---
_id: '7754'
abstract:
- lang: eng
text: Creating a selective gel that filters particles based on their interactions
is a major goal of nanotechnology, with far-reaching implications from drug delivery
to controlling assembly pathways. However, this is particularly difficult when
the particles are larger than the gel’s characteristic mesh size because such
particles cannot passively pass through the gel. Thus, filtering requires the
interacting particles to transiently reorganize the gel’s internal structure.
While significant advances, e.g., in DNA engineering, have enabled the design
of nano-materials with programmable interactions, it is not clear what physical
principles such a designer gel could exploit to achieve selective permeability.
We present an equilibrium mechanism where crosslink binding dynamics are affected
by interacting particles such that particle diffusion is enhanced. In addition
to revealing specific design rules for manufacturing selective gels, our results
have the potential to explain the origin of selective permeability in certain
biological materials, including the nuclear pore complex.
article_number: '4348'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
- first_name: Katharina
full_name: Ribbeck, Katharina
last_name: Ribbeck
citation:
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
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
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.
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.
ista: Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to
the crosslinks of a polymer gel. Nature Communications. 9, 4348.
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).
date_created: 2020-04-30T11:38:01Z
date_published: 2018-10-19T00:00:00Z
date_updated: 2021-01-12T08:15:18Z
day: '19'
doi: 10.1038/s41467-018-06851-5
extern: '1'
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-06851-5
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Enhanced diffusion by binding to the crosslinks of a polymer gel
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '7755'
abstract:
- lang: eng
text: We give a bird's-eye view of the plastic deformation of crystals aimed at
the statistical physics community, as well as a broad introduction to the statistical
theories of forced rigid systems aimed at the plasticity community. Memory effects
in magnets, spin glasses, charge density waves, and dilute colloidal suspensions
are discussed in relation to the onset of plastic yielding in crystals. Dislocation
avalanches and complex dislocation tangles are discussed via a brief introduction
to the renormalization group and scaling. Analogies to emergent scale invariance
in fracture, jamming, coarsening, and a variety of depinning transitions are explored.
Dislocation dynamics in crystals challenge nonequilibrium statistical physics.
Statistical physics provides both cautionary tales of subtle memory effects in
nonequilibrium systems and systematic tools designed to address complex scale-invariant
behavior on multiple length scales and timescales.
article_processing_charge: No
article_type: original
author:
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
- first_name: Matthew K.
full_name: Bierbaum, Matthew K.
last_name: Bierbaum
- first_name: Karin A.
full_name: Dahmen, Karin A.
last_name: Dahmen
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Julia R.
full_name: Greer, Julia R.
last_name: Greer
- first_name: Lorien X.
full_name: Hayden, Lorien X.
last_name: Hayden
- first_name: Jaron P.
full_name: Kent-Dobias, Jaron P.
last_name: Kent-Dobias
- first_name: Edward D.
full_name: Lee, Edward D.
last_name: Lee
- first_name: Danilo B.
full_name: Liarte, Danilo B.
last_name: Liarte
- first_name: Xiaoyue
full_name: Ni, Xiaoyue
last_name: Ni
- first_name: Katherine N.
full_name: Quinn, Katherine N.
last_name: Quinn
- first_name: Archishman
full_name: Raju, Archishman
last_name: Raju
- first_name: D. Zeb
full_name: Rocklin, D. Zeb
last_name: Rocklin
- first_name: Ashivni
full_name: Shekhawat, Ashivni
last_name: Shekhawat
- first_name: Stefano
full_name: Zapperi, Stefano
last_name: Zapperi
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'
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'
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.'
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.'
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.'
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.
date_created: 2020-04-30T11:38:24Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:15:18Z
day: '01'
doi: 10.1146/annurev-matsci-070115-032036
extern: '1'
intvolume: ' 47'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1146/annurev-matsci-070115-032036
month: '07'
oa: 1
oa_version: Published Version
page: 217-246
publication: Annual Review of Materials Research
publication_identifier:
issn:
- 1531-7331
- 1545-4118
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Deformation of crystals: Connections with statistical physics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 47
year: '2017'
...
---
_id: '7756'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Baity-Jesi, Marco
last_name: Baity-Jesi
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
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
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
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.
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.
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.
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.
date_created: 2020-04-30T11:38:38Z
date_published: 2017-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '03'
doi: 10.1007/s10955-016-1703-9
extern: '1'
intvolume: ' 167'
issue: 3-4
language:
- iso: eng
month: '01'
oa_version: None
page: 735-748
publication: Journal of Statistical Physics
publication_identifier:
issn:
- 0022-4715
- 1572-9613
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Emergent SO(3) symmetry of the frictionless shear jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 167
year: '2017'
...
---
_id: '7757'
abstract:
- lang: eng
text: Recent advances in designing metamaterials have demonstrated that global mechanical
properties of disordered spring networks can be tuned by selectively modifying
only a small subset of bonds. Here, using a computationally efficient approach,
we extend this idea to tune more general properties of networks. With nearly complete
success, we are able to produce a strain between any two target nodes in a network
in response to an applied source strain on any other pair of nodes by removing
only ∼1% of the bonds. We are also able to control multiple pairs of target nodes,
each with a different individual response, from a single source, and to tune multiple
independent source/target responses simultaneously into a network. We have fabricated
physical networks in macroscopic 2D and 3D systems that exhibit these responses.
This work is inspired by the long-range coupled conformational changes that constitute
allosteric function in proteins. The fact that allostery is a common means for
regulation in biological molecules suggests that it is a relatively easy property
to develop through evolution. In analogy, our results show that long-range coupled
mechanical responses are similarly easy to achieve in disordered networks.
article_processing_charge: No
article_type: original
author:
- first_name: Jason W.
full_name: Rocks, Jason W.
last_name: Rocks
- first_name: Nidhi
full_name: Pashine, Nidhi
last_name: Pashine
- first_name: Irmgard
full_name: Bischofberger, Irmgard
last_name: Bischofberger
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
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
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
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.
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.
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.
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.
date_created: 2020-04-30T11:38:53Z
date_published: 2017-03-07T00:00:00Z
date_updated: 2021-01-12T08:15:19Z
day: '07'
doi: 10.1073/pnas.1612139114
extern: '1'
intvolume: ' 114'
issue: '10'
language:
- iso: eng
month: '03'
oa_version: None
page: 2520-2525
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Designing allostery-inspired response in mechanical networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7758'
abstract:
- lang: eng
text: Controlling motion at the microscopic scale is a fundamental goal in the development
of biologically inspired systems. We show that the motion of active, self-propelled
colloids can be sufficiently controlled for use as a tool to assemble complex
structures such as braids and weaves out of microscopic filaments. Unlike typical
self-assembly paradigms, these structures are held together by geometric constraints
rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves
precisely controlling the 2D motion of active colloids so that their path has
a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics
simulations that, when the colloids are attached to long semiflexible filaments,
this motion causes the filaments to braid. The ability of the active particles
to provide sufficient force necessary to bend the filaments into a braid depends
on a number of factors, including the self-propulsion mechanism, the properties
of the filament, and the maximum curvature in the braid. Our work demonstrates
that nonequilibrium assembly pathways can be designed using active particles.
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Michael P.
full_name: Brenner, Michael P.
last_name: Brenner
citation:
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
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.
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.
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.
short: C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences
114 (2017) 257–262.
date_created: 2020-04-30T11:39:09Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2021-01-12T08:15:20Z
day: '10'
doi: 10.1073/pnas.1608838114
extern: '1'
intvolume: ' 114'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 257-262
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Using active colloids as machines to weave and braid on the micrometer scale
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '7763'
abstract:
- lang: eng
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.
article_processing_charge: No
article_type: original
author:
- first_name: Richard
full_name: Lombardini, Richard
last_name: Lombardini
- first_name: Ramiro
full_name: Acevedo, Ramiro
last_name: Acevedo
- first_name: Alexander
full_name: Kuczala, Alexander
last_name: Kuczala
- first_name: Kerry P.
full_name: Keys, Kerry P.
last_name: Keys
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Bruce R.
full_name: Johnson, Bruce R.
last_name: Johnson
citation:
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
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
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.
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.
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.
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.
short: R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson,
Journal of Computational Physics 305 (2016) 244–262.
date_created: 2020-04-30T11:40:41Z
date_published: 2016-01-15T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '15'
doi: 10.1016/j.jcp.2015.10.035
extern: '1'
intvolume: ' 305'
language:
- iso: eng
month: '01'
oa_version: None
page: 244-262
publication: Journal of Computational Physics
publication_identifier:
issn:
- 0021-9991
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 305
year: '2016'
...
---
_id: '7764'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
citation:
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
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
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.
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.
ista: Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self
stress in jammed systems. Soft Matter. 12(17), 3982–3990.
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.
date_created: 2020-04-30T11:40:56Z
date_published: 2016-03-14T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '14'
doi: 10.1039/c6sm00094k
extern: '1'
intvolume: ' 12'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 3982-3990
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
related_material:
link:
- relation: other
url: https://doi.org/10.1039/c6sm02496c
status: public
title: Spatial structure of states of self stress in jammed systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '7760'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
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
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.
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.
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.
short: C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy
of Sciences 113 (2016) 9745–9750.
date_created: 2020-04-30T11:39:53Z
date_published: 2016-08-30T00:00:00Z
date_updated: 2021-01-12T08:15:21Z
day: '30'
doi: 10.1073/pnas.1601858113
extern: '1'
intvolume: ' 113'
issue: '35'
language:
- iso: eng
month: '08'
oa_version: None
page: 9745-9750
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Scaling ansatz for the jamming transition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '7761'
abstract:
- lang: eng
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.
article_number: '235501'
article_processing_charge: No
article_type: original
author:
- first_name: Amy L.
full_name: Graves, Amy L.
last_name: Graves
- first_name: Samer
full_name: Nashed, Samer
last_name: Nashed
- first_name: Elliot
full_name: Padgett, Elliot
last_name: Padgett
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: James P.
full_name: Sethna, James P.
last_name: Sethna
citation:
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'
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'
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.'
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.'
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.'
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.'
short: A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna,
Physical Review Letters 116 (2016).
date_created: 2020-04-30T11:40:10Z
date_published: 2016-06-10T00:00:00Z
date_updated: 2021-01-12T08:15:21Z
day: '10'
doi: 10.1103/physrevlett.116.235501
extern: '1'
intvolume: ' 116'
issue: '23'
language:
- iso: eng
month: '06'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Pinning susceptibility: The effect of dilute, quenched disorder on jamming'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2016'
...
---
_id: '7762'
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.
article_number: '088001 '
article_processing_charge: No
article_type: original
author:
- first_name: Jennifer M.
full_name: Rieser, Jennifer M.
last_name: Rieser
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Douglas J.
full_name: Durian, Douglas J.
last_name: Durian
citation:
ama: 'Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy
vector: A threshold-free characterization of local structure in amorphous materials.
Physical Review Letters. 2016;116(8). doi:10.1103/physrevlett.116.088001'
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'
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.'
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.'
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.'
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.'
short: J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters
116 (2016).
date_created: 2020-04-30T11:40:25Z
date_published: 2016-02-23T00:00:00Z
date_updated: 2021-01-12T08:15:22Z
day: '23'
doi: 10.1103/physrevlett.116.088001
extern: '1'
intvolume: ' 116'
issue: '8'
language:
- iso: eng
month: '02'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Divergence of Voronoi cell anisotropy vector: A threshold-free characterization
of local structure in amorphous materials'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2016'
...
---
_id: '7765'
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.'
article_number: '225501'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
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'
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.'
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.'
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.'
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).
date_created: 2020-04-30T11:41:08Z
date_published: 2015-06-04T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '04'
doi: 10.1103/physrevlett.114.225501
extern: '1'
intvolume: ' 114'
issue: '22'
language:
- iso: eng
month: '06'
oa_version: None
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'The principle of independent bond-level response: Tuning by pruning to exploit
disorder for global behavior'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2015'
...
---
_id: '7766'
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.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
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
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
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.
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.
ista: Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations
in jammed sphere packings. Soft Matter. 11(14), 2745–2751.
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.
date_created: 2020-04-30T11:41:23Z
date_published: 2015-02-15T00:00:00Z
date_updated: 2021-01-12T08:15:23Z
day: '15'
doi: 10.1039/c4sm02905d
extern: '1'
intvolume: ' 11'
issue: '14'
language:
- iso: eng
month: '02'
oa_version: None
page: 2745-2751
publication: Soft Matter
publication_identifier:
issn:
- 1744-683X
- 1744-6848
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
status: public
title: Disordered surface vibrations in jammed sphere packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '7767'
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.
article_number: '032706'
article_processing_charge: No
article_type: original
author:
- first_name: Ruben
full_name: van Drongelen, Ruben
last_name: van Drongelen
- first_name: Anshuman
full_name: Pal, Anshuman
last_name: Pal
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
citation:
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
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
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.
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.
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.
short: R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).
date_created: 2020-04-30T11:41:38Z
date_published: 2015-03-01T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '01'
doi: 10.1103/physreve.91.032706
extern: '1'
intvolume: ' 91'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Collective dynamics of soft active particles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2015'
...
---
_id: '7779'
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."
article_processing_charge: No
arxiv: 1
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
citation:
ama: 'Goodrich CP. Unearthing the anticrystal: Criticality in the linear response
of disordered solids. arXiv:151008820. 2015.'
apa: 'Goodrich, C. P. (2015). Unearthing the anticrystal: Criticality in the linear
response of disordered solids. arXiv:1510.08820.'
chicago: 'Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the
Linear Response of Disordered Solids.” ArXiv:1510.08820, 2015.'
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, .'
mla: '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).
date_created: 2020-04-30T12:16:18Z
date_published: 2015-10-29T00:00:00Z
date_updated: 2021-01-12T08:15:28Z
day: '29'
extern: '1'
external_id:
arxiv:
- '1510.08820'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1510.08820
month: '10'
oa: 1
oa_version: Preprint
page: '242'
publication: arXiv:1510.08820
publication_status: published
status: public
title: 'Unearthing the anticrystal: Criticality in the linear response of disordered
solids'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '7768'
abstract:
- lang: eng
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.
article_number: '062305'
article_processing_charge: No
article_type: original
author:
- first_name: Matthew A.
full_name: Lohr, Matthew A.
last_name: Lohr
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Raman
full_name: Ganti, Raman
last_name: Ganti
- first_name: Matthew D.
full_name: Gratale, Matthew D.
last_name: Gratale
- first_name: Zoey S.
full_name: Davidson, Zoey S.
last_name: Davidson
- first_name: Kevin B.
full_name: Aptowicz, Kevin B.
last_name: Aptowicz
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Daniel M.
full_name: Sussman, Daniel M.
last_name: Sussman
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
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
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
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.
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.
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.
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).
date_created: 2020-04-30T11:41:54Z
date_published: 2014-12-05T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '05'
doi: 10.1103/physreve.90.062305
extern: '1'
intvolume: ' 90'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Vibrational and structural signatures of the crossover between dense glassy
and sparse gel-like attractive colloidal packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7769'
abstract:
- lang: eng
text: 'Athermal packings of soft repulsive spheres exhibit a sharp jamming transition
in the thermodynamic limit. Upon further compression, various structural and mechanical
properties display clean power-law behavior over many decades in pressure. As
with any phase transition, the rounding of such behavior in finite systems close
to the transition plays an important role in understanding the nature of the transition
itself. The situation for jamming is surprisingly rich: the assumption that jammed
packings are isotropic is only strictly true in the large-size limit, and finite-size
has a profound effect on the very meaning of jamming. Here, we provide a comprehensive
numerical study of finite-size effects in sphere packings above the jamming transition,
focusing on stability as well as the scaling of the contact number and the elastic
response.'
article_number: '022138'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Simon
full_name: Dagois-Bohy, Simon
last_name: Dagois-Bohy
- first_name: Brian P.
full_name: Tighe, Brian P.
last_name: Tighe
- first_name: Martin
full_name: van Hecke, Martin
last_name: van Hecke
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming
in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 2014;90(2). doi:10.1103/physreve.90.022138'
apa: 'Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J.,
& Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.90.022138'
chicago: 'Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke,
Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/physreve.90.022138.'
ieee: 'C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and
S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations,
and scaling,” Physical Review E, vol. 90, no. 2. American Physical Society,
2014.'
ista: 'Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014.
Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical
Review E. 90(2), 022138.'
mla: 'Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy,
Fluctuations, and Scaling.” Physical Review E, vol. 90, no. 2, 022138,
American Physical Society, 2014, doi:10.1103/physreve.90.022138.'
short: C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel,
Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:09Z
date_published: 2014-08-27T00:00:00Z
date_updated: 2021-01-12T08:15:24Z
day: '27'
doi: 10.1103/physreve.90.022138
extern: '1'
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: 'Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...