--- _id: '12708' abstract: - lang: eng text: Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter. acknowledgement: 'All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).' article_processing_charge: No article_type: original author: - first_name: Nuno A.M. full_name: Araújo, Nuno A.M. last_name: Araújo - first_name: Liesbeth M.C. full_name: Janssen, Liesbeth M.C. last_name: Janssen - first_name: Thomas full_name: Barois, Thomas last_name: Barois - first_name: Guido full_name: Boffetta, Guido last_name: Boffetta - first_name: Itai full_name: Cohen, Itai last_name: Cohen - first_name: Alessandro full_name: Corbetta, Alessandro last_name: Corbetta - first_name: Olivier full_name: Dauchot, Olivier last_name: Dauchot - first_name: Marjolein full_name: Dijkstra, Marjolein last_name: Dijkstra - first_name: William M. full_name: Durham, William M. last_name: Durham - first_name: Audrey full_name: Dussutour, Audrey last_name: Dussutour - first_name: Simon full_name: Garnier, Simon last_name: Garnier - first_name: Hanneke full_name: Gelderblom, Hanneke last_name: Gelderblom - first_name: Ramin full_name: Golestanian, Ramin last_name: Golestanian - first_name: Lucio full_name: Isa, Lucio last_name: Isa - first_name: Gijsje H. full_name: Koenderink, Gijsje H. last_name: Koenderink - first_name: Hartmut full_name: Löwen, Hartmut last_name: Löwen - first_name: Ralf full_name: Metzler, Ralf last_name: Metzler - first_name: Marco full_name: Polin, Marco last_name: Polin - first_name: C. Patrick full_name: Royall, C. Patrick last_name: Royall - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Anupam full_name: Sengupta, Anupam last_name: Sengupta - first_name: Cécile full_name: Sykes, Cécile last_name: Sykes - first_name: Vito full_name: Trianni, Vito last_name: Trianni - first_name: Idan full_name: Tuval, Idan last_name: Tuval - first_name: Nicolas full_name: Vogel, Nicolas last_name: Vogel - first_name: Julia M. full_name: Yeomans, Julia M. last_name: Yeomans - first_name: Iker full_name: Zuriguel, Iker last_name: Zuriguel - first_name: Alvaro full_name: Marin, Alvaro last_name: Marin - first_name: Giorgio full_name: Volpe, Giorgio last_name: Volpe citation: ama: Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e apa: Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e chicago: Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e. ieee: N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023. ista: Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704. mla: Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e. short: N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704. date_created: 2023-03-05T23:01:06Z date_published: 2023-02-06T00:00:00Z date_updated: 2023-08-01T13:28:39Z day: '06' ddc: - '540' department: - _id: AnSa doi: 10.1039/d2sm01562e ec_funded: 1 external_id: arxiv: - '2204.10059' isi: - '000940388100001' file: - access_level: open_access checksum: af95aa18b9b01e32fb8f13477c0e2687 content_type: application/pdf creator: cchlebak date_created: 2023-03-07T09:19:41Z date_updated: 2023-03-07T09:19:41Z file_id: '12711' file_name: 2023_SoftMatter_Araujo.pdf file_size: 3581939 relation: main_file success: 1 file_date_updated: 2023-03-07T09:19:41Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '02' oa: 1 oa_version: Published Version page: 1695-1704 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Steering self-organisation through confinement 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2023' ... --- _id: '14087' abstract: - lang: eng text: Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter. acknowledgement: J. Rø and L. A. acknowledge support from the Research Council of Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab). A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142 and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jonas full_name: Rønning, Jonas last_name: Rønning - first_name: Julian B full_name: Renaud, Julian B id: 7af6767d-14eb-11ed-b536-a32449ae867c last_name: Renaud - first_name: Amin full_name: Doostmohammadi, Amin last_name: Doostmohammadi - first_name: Luiza full_name: Angheluta, Luiza last_name: Angheluta citation: ama: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 2023;39:7513-7527. doi:10.1039/d3sm00316g apa: Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g chicago: Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g. ieee: J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023. ista: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 39, 7513–7527. mla: Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” Soft Matter, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g. short: J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527. date_created: 2023-08-20T22:01:15Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-30T12:49:24Z day: '01' ddc: - '540' department: - _id: GradSch doi: 10.1039/d3sm00316g external_id: arxiv: - '2303.07063' isi: - '001035766100001' file: - access_level: open_access checksum: b936747170d0b708172b518078c4081a content_type: application/pdf creator: dernst date_created: 2024-01-30T12:48:24Z date_updated: 2024-01-30T12:48:24Z file_id: '14908' file_name: 2023_SoftMatter_Ronning.pdf file_size: 7660662 relation: main_file success: 1 file_date_updated: 2024-01-30T12:48:24Z has_accepted_license: '1' intvolume: ' 39' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 7513-7527 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Spontaneous flows and dynamics of full-integer topological defects in polar active matter 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: 39 year: '2023' ... --- _id: '10339' abstract: - lang: eng text: We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation. acknowledgement: We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.), the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council (Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan Palaia for fruitful discussions. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Vanhille-Campos, Christian last_name: Vanhille-Campos - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 2021;17(14):3798-3806. doi:10.1039/d0sm02012e apa: Vanhille-Campos, C., & Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm02012e chicago: Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” Soft Matter. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d0sm02012e. ieee: C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” Soft Matter, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021. ista: Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806. mla: Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” Soft Matter, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:10.1039/d0sm02012e. short: C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806. date_created: 2021-11-25T16:06:42Z date_published: 2021-02-16T00:00:00Z date_updated: 2021-11-30T08:20:09Z day: '16' doi: 10.1039/d0sm02012e extern: '1' external_id: pmid: - '33629089' intvolume: ' 17' issue: '14' keyword: - condensed matter physics - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e month: '02' oa: 1 oa_version: Published Version page: 3798-3806 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' related_material: link: - relation: earlier_version url: https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2 scopus_import: '1' status: public title: Modelling the dynamics of vesicle reshaping and scission under osmotic shocks tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 17 year: '2021' ... --- _id: '10204' abstract: - lang: eng text: Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals. acknowledgement: MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant no. 788183 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. article_processing_charge: No article_type: original author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mohammad full_name: Saadatfar, Mohammad last_name: Saadatfar citation: ama: Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 2021;17(40):9107-9115. doi:10.1039/d1sm00774b apa: Osang, G. F., Edelsbrunner, H., & Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/d1sm00774b chicago: Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter. Royal Society of Chemistry , 2021. https://doi.org/10.1039/d1sm00774b. ieee: G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” Soft Matter, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021. ista: Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115. mla: Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” Soft Matter, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:10.1039/d1sm00774b. short: G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115. date_created: 2021-10-31T23:01:30Z date_published: 2021-10-20T00:00:00Z date_updated: 2023-10-03T09:24:27Z day: '20' ddc: - '540' department: - _id: HeEd doi: 10.1039/d1sm00774b ec_funded: 1 external_id: isi: - '000700090000001' pmid: - '34569592' file: - access_level: open_access checksum: b4da0c420530295e61b153960f6cb350 content_type: application/pdf creator: dernst date_created: 2023-10-03T09:21:42Z date_updated: 2023-10-03T09:21:42Z file_id: '14385' file_name: 2021_SoftMatter_acceptedversion_Osang.pdf file_size: 4678788 relation: main_file success: 1 file_date_updated: 2023-10-03T09:21:42Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '40' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 9107-9115 pmid: 1 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Topological signatures and stability of hexagonal close packing and Barlow stackings type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2021' ... --- _id: '10341' abstract: - lang: eng text: Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes. acknowledgement: We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.). article_processing_charge: No article_type: original author: - first_name: V. E. full_name: Debets, V. E. last_name: Debets - first_name: L. M. C. full_name: Janssen, L. M. C. last_name: Janssen - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 2020;16(47):10628-10639. doi:10.1039/d0sm00712a apa: Debets, V. E., Janssen, L. M. C., & Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d0sm00712a chicago: Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter. Royal Society of Chemistry, 2020. https://doi.org/10.1039/d0sm00712a. ieee: V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” Soft Matter, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020. ista: Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639. mla: Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” Soft Matter, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:10.1039/d0sm00712a. short: V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639. date_created: 2021-11-26T06:29:41Z date_published: 2020-10-06T00:00:00Z date_updated: 2021-11-26T07:00:33Z day: '06' doi: 10.1039/d0sm00712a extern: '1' external_id: pmid: - '33084724' intvolume: ' 16' issue: '47' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1 month: '10' oa: 1 oa_version: Published Version page: 10628-10639 pmid: 1 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 16 year: '2020' ... --- _id: '9054' abstract: - lang: eng text: 'The fundamental and practical importance of particle stabilization has motivated various characterization methods for studying polymer brushes on particle surfaces. In this work, we show how one can perform sensitive measurements of neutral polymer coating on colloidal particles using a commercial zetameter and salt solutions. By systematically varying the Debye length, we study the mobility of the polymer-coated particles in an applied electric field and show that the electrophoretic mobility of polymer-coated particles normalized by the mobility of non-coated particles is entirely controlled by the polymer brush and independent of the native surface charge, here controlled with pH, or the surface–ion interaction. Our result is rationalized with a simple hydrodynamic model, allowing for the estimation of characteristics of the polymer coating: the brush length L, and the Brinkman length ξ, determined by its resistance to flows. We demonstrate that the Debye layer provides a convenient and faithful probe to the characterization of polymer coatings on particles. Because the method simply relies on a conventional zetameter, it is widely accessible and offers a practical tool to rapidly probe neutral polymer brushes, an asset in the development and utilization of polymer-coated colloidal particles.' article_processing_charge: No article_type: original author: - first_name: Mena full_name: Youssef, Mena last_name: Youssef - first_name: Alexandre full_name: Morin, Alexandre last_name: Morin - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. Soft Matter. 2020;16(17):4274-4282. doi:10.1039/c9sm01850f apa: Youssef, M., Morin, A., Aubret, A., Sacanna, S., & Palacci, J. A. (2020). Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c9sm01850f chicago: Youssef, Mena, Alexandre Morin, Antoine Aubret, Stefano Sacanna, and Jérémie A Palacci. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” Soft Matter. Royal Society of Chemistry , 2020. https://doi.org/10.1039/c9sm01850f. ieee: M. Youssef, A. Morin, A. Aubret, S. Sacanna, and J. A. Palacci, “Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt,” Soft Matter, vol. 16, no. 17. Royal Society of Chemistry , pp. 4274–4282, 2020. ista: Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. 2020. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. Soft Matter. 16(17), 4274–4282. mla: Youssef, Mena, et al. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” Soft Matter, vol. 16, no. 17, Royal Society of Chemistry , 2020, pp. 4274–82, doi:10.1039/c9sm01850f. short: M. Youssef, A. Morin, A. Aubret, S. Sacanna, J.A. Palacci, Soft Matter 16 (2020) 4274–4282. date_created: 2021-02-01T13:45:11Z date_published: 2020-05-07T00:00:00Z date_updated: 2023-02-23T13:47:45Z day: '07' doi: 10.1039/c9sm01850f extern: '1' external_id: pmid: - '32307507' intvolume: ' 16' issue: '17' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng month: '05' oa_version: None page: 4274-4282 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 16 year: '2020' ... --- _id: '5817' abstract: - lang: eng text: We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion. article_processing_charge: No article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: A. full_name: Sakashita, A. last_name: Sakashita - first_name: H. full_name: Noguchi, H. last_name: Noguchi - first_name: P. full_name: Ziherl, P. last_name: Ziherl citation: ama: Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h apa: Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h chicago: Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h. ieee: B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019. ista: Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614. mla: Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h. short: B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614. date_created: 2019-01-11T07:37:47Z date_published: 2019-01-10T00:00:00Z date_updated: 2023-09-13T08:47:16Z day: '10' ddc: - '530' department: - _id: GaTk doi: 10.1039/c8sm01956h external_id: isi: - '000457329700003' pmid: - '30629082' file: - access_level: open_access checksum: 614c337d6424ccd3d48d1b1f9513510d content_type: application/pdf creator: bkavcic date_created: 2020-10-09T11:00:05Z date_updated: 2020-10-09T11:00:05Z file_id: '8641' file_name: lmt_sftmtr_V8.pdf file_size: 5370762 relation: main_file success: 1 file_date_updated: 2020-10-09T11:00:05Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/3.0/ month: '01' oa: 1 oa_version: Submitted Version page: 602-614 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Limiting shapes of confined lipid vesicles tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) short: CC BY-NC-ND (3.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2019' ... --- _id: '9053' abstract: - lang: eng text: The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena. article_processing_charge: No article_type: original author: - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 2018;14(47):9577-9588. doi:10.1039/c8sm01760c apa: Aubret, A., & Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c8sm01760c chicago: Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter. Royal Society of Chemistry , 2018. https://doi.org/10.1039/c8sm01760c. ieee: A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” Soft Matter, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018. ista: Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588. mla: Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:10.1039/c8sm01760c. short: A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588. date_created: 2021-02-01T13:44:41Z date_published: 2018-12-21T00:00:00Z date_updated: 2023-02-23T13:47:43Z day: '21' doi: 10.1039/c8sm01760c extern: '1' external_id: arxiv: - '1909.11121' pmid: - '30456407' intvolume: ' 14' issue: '47' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1909.11121 month: '12' oa: 1 oa_version: Preprint page: 9577-9588 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Diffusiophoretic design of self-spinning microgears from colloidal microswimmers type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 14 year: '2018' ... --- _id: '10375' abstract: - lang: eng text: 'Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts.' acknowledgement: This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program. article_processing_charge: No article_type: original author: - first_name: Afshin full_name: Vahid, Afshin last_name: Vahid - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Timon full_name: Idema, Timon last_name: Idema citation: ama: Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h apa: Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c7sm00433h chicago: Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sm00433h. ieee: A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017. ista: Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930. mla: Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:10.1039/c7sm00433h. short: A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930. date_created: 2021-11-29T10:00:39Z date_published: 2017-06-15T00:00:00Z date_updated: 2021-11-29T10:33:36Z day: '15' doi: 10.1039/c7sm00433h extern: '1' external_id: arxiv: - '1703.00776' pmid: - '28677712' intvolume: ' 13' issue: '28' keyword: - condensed matter physics - general chemistry language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ main_file_link: - open_access: '1' url: https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H month: '06' oa: 1 oa_version: Published Version page: 4924-4930 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Curvature variation controls particle aggregation on fluid vesicles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 13 year: '2017' ... --- _id: '10381' abstract: - lang: eng text: We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand–receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand–receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion. article_processing_charge: No article_type: original author: - first_name: Stephan Jan full_name: Bachmann, Stephan Jan last_name: Bachmann - first_name: Jurij full_name: Kotar, Jurij last_name: Kotar - first_name: Lucia full_name: Parolini, Lucia last_name: Parolini - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Pietro full_name: Cicuta, Pietro last_name: Cicuta - first_name: Lorenzo full_name: Di Michele, Lorenzo last_name: Di Michele - first_name: Bortolo Matteo full_name: Mognetti, Bortolo Matteo last_name: Mognetti citation: ama: Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 2016;12(37):7804-7817. doi:10.1039/c6sm01515h apa: Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., & Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c6sm01515h chicago: Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter. Royal Society of Chemistry, 2016. https://doi.org/10.1039/c6sm01515h. ieee: S. J. Bachmann et al., “Melting transition in lipid vesicles functionalised by mobile DNA linkers,” Soft Matter, vol. 12, no. 37. Royal Society of Chemistry, pp. 7804–7817, 2016. ista: Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 12(37), 7804–7817. mla: Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” Soft Matter, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:10.1039/c6sm01515h. short: S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817. date_created: 2021-11-29T11:09:55Z date_published: 2016-08-19T00:00:00Z date_updated: 2021-11-29T13:09:00Z day: '19' doi: 10.1039/c6sm01515h extern: '1' external_id: arxiv: - '1608.05788' pmid: - '27722701' intvolume: ' 12' issue: '37' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.05788 month: '08' oa: 1 oa_version: Preprint page: 7804-7817 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Melting transition in lipid vesicles functionalised by mobile DNA linkers type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 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: '9051' abstract: - lang: eng text: 'Biological systems often involve the self-assembly of basic components into complex and functioning structures. Artificial systems that mimic such processes can provide a well-controlled setting to explore the principles involved and also synthesize useful micromachines. Our experiments show that immotile, but active, components self-assemble into two types of structure that exhibit the fundamental forms of motility: translation and rotation. Specifically, micron-scale metallic rods are designed to induce extensile surface flows in the presence of a chemical fuel; these rods interact with each other and pair up to form either a swimmer or a rotor. Such pairs can transition reversibly between these two configurations, leading to kinetics reminiscent of bacterial run-and-tumble motion.' article_processing_charge: No article_type: original author: - first_name: Megan S. full_name: Davies Wykes, Megan S. last_name: Davies Wykes - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Takuji full_name: Adachi, Takuji last_name: Adachi - first_name: Leif full_name: Ristroph, Leif last_name: Ristroph - first_name: Xiao full_name: Zhong, Xiao last_name: Zhong - first_name: Michael D. full_name: Ward, Michael D. last_name: Ward - first_name: Jun full_name: Zhang, Jun last_name: Zhang - first_name: Michael J. full_name: Shelley, Michael J. last_name: Shelley citation: ama: Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. 2016;12(20):4584-4589. doi:10.1039/c5sm03127c apa: Davies Wykes, M. S., Palacci, J. A., Adachi, T., Ristroph, L., Zhong, X., Ward, M. D., … Shelley, M. J. (2016). Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c5sm03127c chicago: Davies Wykes, Megan S., Jérémie A Palacci, Takuji Adachi, Leif Ristroph, Xiao Zhong, Michael D. Ward, Jun Zhang, and Michael J. Shelley. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” Soft Matter. Royal Society of Chemistry, 2016. https://doi.org/10.1039/c5sm03127c. ieee: M. S. Davies Wykes et al., “Dynamic self-assembly of microscale rotors and swimmers,” Soft Matter, vol. 12, no. 20. Royal Society of Chemistry, pp. 4584–4589, 2016. ista: Davies Wykes MS, Palacci JA, Adachi T, Ristroph L, Zhong X, Ward MD, Zhang J, Shelley MJ. 2016. Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. 12(20), 4584–4589. mla: Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” Soft Matter, vol. 12, no. 20, Royal Society of Chemistry, 2016, pp. 4584–89, doi:10.1039/c5sm03127c. short: M.S. Davies Wykes, J.A. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward, J. Zhang, M.J. Shelley, Soft Matter 12 (2016) 4584–4589. date_created: 2021-02-01T13:44:00Z date_published: 2016-05-28T00:00:00Z date_updated: 2023-02-23T13:47:38Z day: '28' doi: 10.1039/c5sm03127c extern: '1' external_id: arxiv: - '1509.06330' pmid: - '27121100' intvolume: ' 12' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.06330 month: '05' oa: 1 oa_version: Preprint page: 4584-4589 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Dynamic self-assembly of microscale rotors and swimmers type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 12 year: '2016' ... --- _id: '9052' abstract: - lang: eng text: We describe colloidal Janus particles with metallic and dielectric faces that swim vigorously when illuminated by defocused optical tweezers without consuming any chemical fuel. Rather than wandering randomly, these optically-activated colloidal swimmers circulate back and forth through the beam of light, tracing out sinuous rosette patterns. We propose a model for this mode of light-activated transport that accounts for the observed behavior through a combination of self-thermophoresis and optically-induced torque. In the deterministic limit, this model yields trajectories that resemble rosette curves known as hypotrochoids. article_processing_charge: No article_type: original author: - first_name: Henrique full_name: Moyses, Henrique last_name: Moyses - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: David G. full_name: Grier, David G. last_name: Grier citation: ama: Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. 2016;12(30):6357-6364. doi:10.1039/c6sm01163b apa: Moyses, H., Palacci, J. A., Sacanna, S., & Grier, D. G. (2016). Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c6sm01163b chicago: Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” Soft Matter. Royal Society of Chemistry , 2016. https://doi.org/10.1039/c6sm01163b. ieee: H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam,” Soft Matter, vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016. ista: Moyses H, Palacci JA, Sacanna S, Grier DG. 2016. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. 12(30), 6357–6364. mla: Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” Soft Matter, vol. 12, no. 30, Royal Society of Chemistry , 2016, pp. 6357–64, doi:10.1039/c6sm01163b. short: H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364. date_created: 2021-02-01T13:44:15Z date_published: 2016-08-14T00:00:00Z date_updated: 2023-02-23T13:47:40Z day: '14' doi: 10.1039/c6sm01163b extern: '1' external_id: arxiv: - '1609.01497' pmid: - '27338294' intvolume: ' 12' issue: '30' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.01497 month: '08' oa: 1 oa_version: Preprint page: 6357-6364 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 12 year: '2016' ... --- _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: '9050' abstract: - lang: eng text: Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter. article_number: '1784' article_processing_charge: No article_type: original author: - first_name: Daisuke full_name: Takagi, Daisuke last_name: Takagi - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Adam B. full_name: Braunschweig, Adam B. last_name: Braunschweig - first_name: Michael J. full_name: Shelley, Michael J. last_name: Shelley - first_name: Jun full_name: Zhang, Jun last_name: Zhang citation: ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d. ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter, vol. 10, no. 11. Royal Society of Chemistry , 2014. ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784. mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:10.1039/c3sm52815d. short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014). date_created: 2021-02-01T13:43:31Z date_published: 2014-03-21T00:00:00Z date_updated: 2023-02-23T13:47:35Z day: '21' doi: 10.1039/c3sm52815d extern: '1' external_id: arxiv: - '1309.5662' pmid: - '24800268' intvolume: ' 10' issue: '11' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.5662 month: '03' oa: 1 oa_version: Preprint pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Hydrodynamic capture of microswimmers into sphere-bound orbits type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 10 year: '2014' ... --- _id: '10386' abstract: - lang: eng text: In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR 0846426. The authors thank J. C. Pàmies for many fruitful discussions on the subject. article_number: '6677' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 2013;9(29). doi:10.1039/c3sm50188d apa: Šarić, A., & Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm50188d chicago: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm50188d. ieee: A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” Soft Matter, vol. 9, no. 29. Royal Society of Chemistry, 2013. ista: Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677. mla: Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” Soft Matter, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:10.1039/c3sm50188d. short: A. Šarić, A. Cacciuto, Soft Matter 9 (2013). date_created: 2021-11-29T14:06:32Z date_published: 2013-05-03T00:00:00Z date_updated: 2021-11-29T14:29:31Z day: '03' doi: 10.1039/c3sm50188d extern: '1' intvolume: ' 9' issue: '29' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - url: https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d month: '05' oa_version: None publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Self-assembly of nanoparticles adsorbed on fluid and elastic membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9 year: '2013' ... --- _id: '10385' abstract: - lang: eng text: We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials. acknowledgement: This work was supported by the National Science Foundation under Career Grant no. DMR-0846426. article_processing_charge: No article_type: original author: - first_name: Joseph A. full_name: Napoli, Joseph A. last_name: Napoli - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. Soft Matter. 2013;9(37):8881-8886. doi:10.1039/c3sm51495a apa: Napoli, J. A., Šarić, A., & Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51495a chicago: Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51495a. ieee: J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” Soft Matter, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013. ista: Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886. mla: Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” Soft Matter, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:10.1039/c3sm51495a. short: J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886. date_created: 2021-11-29T13:31:24Z date_published: 2013-08-08T00:00:00Z date_updated: 2021-11-29T14:05:23Z day: '08' doi: 10.1039/c3sm51495a extern: '1' intvolume: ' 9' issue: '37' keyword: - condensed matter physics - general chemistry language: - iso: eng month: '08' oa_version: None page: 8881-8886 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Collapsing nanoparticle-laden nanotubes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9 year: '2013' ... --- _id: '7775' abstract: - lang: eng text: As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition. article_number: '11000' article_processing_charge: No article_type: original author: - first_name: Samuel S. full_name: Schoenholz, Samuel S. last_name: Schoenholz - 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: Oleg full_name: Kogan, Oleg last_name: Kogan - 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: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. Stability of jammed packings II: The transverse length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51096d' apa: 'Schoenholz, S. S., Goodrich, C. P., Kogan, O., Liu, A. J., & Nagel, S. R. (2013). Stability of jammed packings II: The transverse length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51096d' chicago: 'Schoenholz, Samuel S., Carl Peter Goodrich, Oleg Kogan, Andrea J. Liu, and Sidney R. Nagel. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51096d.' ieee: 'S. S. Schoenholz, C. P. Goodrich, O. Kogan, A. J. Liu, and S. R. Nagel, “Stability of jammed packings II: The transverse length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Schoenholz SS, Goodrich CP, Kogan O, Liu AJ, Nagel SR. 2013. Stability of jammed packings II: The transverse length scale. Soft Matter. 9(46), 11000.' mla: 'Schoenholz, Samuel S., et al. “Stability of Jammed Packings II: The Transverse Length Scale.” Soft Matter, vol. 9, no. 46, 11000, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51096d.' short: S.S. Schoenholz, C.P. Goodrich, O. Kogan, A.J. Liu, S.R. Nagel, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:58Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51096d extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings II: The transverse length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '7774' abstract: - lang: eng text: In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*. article_number: '10993' 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: Wouter G. full_name: Ellenbroek, Wouter G. last_name: Ellenbroek - first_name: Andrea J. full_name: Liu, Andrea J. last_name: Liu citation: ama: 'Goodrich CP, Ellenbroek WG, Liu AJ. Stability of jammed packings I: The rigidity length scale. Soft Matter. 2013;9(46). doi:10.1039/c3sm51095f' apa: 'Goodrich, C. P., Ellenbroek, W. G., & Liu, A. J. (2013). Stability of jammed packings I: The rigidity length scale. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c3sm51095f' chicago: 'Goodrich, Carl Peter, Wouter G. Ellenbroek, and Andrea J. Liu. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3sm51095f.' ieee: 'C. P. Goodrich, W. G. Ellenbroek, and A. J. Liu, “Stability of jammed packings I: The rigidity length scale,” Soft Matter, vol. 9, no. 46. Royal Society of Chemistry, 2013.' ista: 'Goodrich CP, Ellenbroek WG, Liu AJ. 2013. Stability of jammed packings I: The rigidity length scale. Soft Matter. 9(46), 10993.' mla: 'Goodrich, Carl Peter, et al. “Stability of Jammed Packings I: The Rigidity Length Scale.” Soft Matter, vol. 9, no. 46, 10993, Royal Society of Chemistry, 2013, doi:10.1039/c3sm51095f.' short: C.P. Goodrich, W.G. Ellenbroek, A.J. Liu, Soft Matter 9 (2013). date_created: 2020-04-30T11:43:42Z date_published: 2013-10-08T00:00:00Z date_updated: 2021-01-12T08:15:27Z day: '08' doi: 10.1039/c3sm51095f extern: '1' intvolume: ' 9' issue: '46' language: - iso: eng month: '10' oa_version: None publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Stability of jammed packings I: The rigidity length scale' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '9049' abstract: - lang: eng text: 'Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.' article_processing_charge: No article_type: original author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Cécile full_name: Cottin-Bizonne, Cécile last_name: Cottin-Bizonne - first_name: Christophe full_name: Ybert, Christophe last_name: Ybert - first_name: Lydéric full_name: Bocquet, Lydéric last_name: Bocquet citation: ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 2012;8(4):980-994. doi:10.1039/c1sm06395b apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm06395b chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter. Royal Society of Chemistry, 2012. https://doi.org/10.1039/c1sm06395b. ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” Soft Matter, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012. ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994. mla: Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” Soft Matter, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:10.1039/c1sm06395b. short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994. date_created: 2021-02-01T13:43:10Z date_published: 2012-01-28T00:00:00Z date_updated: 2023-02-23T13:47:31Z day: '28' doi: 10.1039/c1sm06395b extern: '1' intvolume: ' 8' issue: '4' language: - iso: eng month: '01' oa_version: None page: 980-994 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 8 year: '2012' ... --- _id: '10389' abstract: - lang: eng text: We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies and William L. Miller for helpful discussions. article_number: '8324' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 2011;7(18). doi:10.1039/c1sm05773a apa: Šarić, A., & Cacciuto, A. (2011). Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c1sm05773a chicago: Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1sm05773a. ieee: A. Šarić and A. Cacciuto, “Soft elastic surfaces as a platform for particle self-assembly,” Soft Matter, vol. 7, no. 18. Royal Society of Chemistry, 2011. ista: Šarić A, Cacciuto A. 2011. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 7(18), 8324. mla: Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” Soft Matter, vol. 7, no. 18, 8324, Royal Society of Chemistry, 2011, doi:10.1039/c1sm05773a. short: A. Šarić, A. Cacciuto, Soft Matter 7 (2011). date_created: 2021-11-29T14:33:18Z date_published: 2011-08-08T00:00:00Z date_updated: 2021-11-29T15:12:10Z day: '08' doi: 10.1039/c1sm05773a extern: '1' external_id: arxiv: - '1106.2995' intvolume: ' 7' issue: '18' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1106.2995 month: '08' oa: 1 oa_version: Preprint publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Soft elastic surfaces as a platform for particle self-assembly type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 7 year: '2011' ... --- _id: '10127' abstract: - lang: eng text: We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions. article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. Soft Matter. 2010;7(5):1874-1878. doi:10.1039/c0sm01143f apa: Šarić, A., & Cacciuto, A. (2010). Particle self-assembly on soft elastic shells. Soft Matter. Royal Society of Chemistry (RSC). https://doi.org/10.1039/c0sm01143f chicago: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” Soft Matter. Royal Society of Chemistry (RSC), 2010. https://doi.org/10.1039/c0sm01143f. ieee: A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,” Soft Matter, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878, 2010. ista: Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells. Soft Matter. 7(5), 1874–1878. mla: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” Soft Matter, vol. 7, no. 5, Royal Society of Chemistry (RSC), 2010, pp. 1874–78, doi:10.1039/c0sm01143f. short: A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878. date_created: 2021-10-12T08:34:23Z date_published: 2010-12-23T00:00:00Z date_updated: 2021-10-12T09:49:27Z day: '23' doi: 10.1039/c0sm01143f extern: '1' external_id: arxiv: - '1010.2453' intvolume: ' 7' issue: '5' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1010.2453 month: '12' oa: 1 oa_version: Preprint page: 1874-1878 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry (RSC) quality_controlled: '1' status: public title: Particle self-assembly on soft elastic shells type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 7 year: '2010' ...