[{"arxiv":1,"quality_controlled":"1","status":"public","corr_author":"1","file":[{"success":1,"date_created":"2025-12-30T10:16:40Z","content_type":"application/pdf","file_name":"2025_SoftMatter_MunozBasagoiti.pdf","date_updated":"2025-12-30T10:16:40Z","creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"20912","file_size":4841140,"checksum":"590bedad19b6f6d40a7ee036a056a6d9"}],"oa":1,"type":"journal_article","abstract":[{"text":"Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations. Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations, by providing a pedagogical examination of membrane tether pulling, shape and mechanics of membrane tubes, and membrane fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.","lang":"eng"}],"date_created":"2025-09-10T05:34:36Z","month":"07","title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","ddc":["540"],"article_type":"original","author":[{"orcid":"0000-0003-1483-1457","last_name":"Muñoz Basagoiti","first_name":"Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","full_name":"Muñoz Basagoiti, Maitane"},{"orcid":"0000-0001-8501-6017","last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"orcid":"0000-0003-3441-1337","first_name":"Billie","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"first_name":"Miguel","last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel"},{"full_name":"Prada, Adam","id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9","last_name":"Prada","first_name":"Adam"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes"}],"doi":"10.1039/d5sm00148j","year":"2025","day":"28","page":"7736-7756","scopus_import":"1","ec_funded":1,"oa_version":"Published Version","volume":21,"date_published":"2025-07-28T00:00:00Z","publication_status":"published","publisher":"Royal Society of Chemistry","acknowledgement":"We thank Oded Farago, Angelo Cacciuto, Jeriann Beiter and Pietro Sillano for helpful discussions and a critical reading of the manuscript. MMB and AP acknowledge funding by the European Unions Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. FF acknowledges financial support by the NOMIS foundation. BM and AŠ acknowledge funding by ERC Starting Grant “NEPA” 802960. MA and AŠ acknowledge funding by the Volkswagen Foundation Grant Az 96727.","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"publication":"Soft Matter","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2025-12-30T10:16:40Z","intvolume":"        21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-30T10:16:52Z","article_processing_charge":"Yes (via OA deal)","_id":"20318","issue":"40","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid","has_accepted_license":"1","external_id":{"arxiv":["2502.09798"],"isi":["001562846800001"]},"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"ieee":"M. Muñoz Basagoiti, F. F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, and A. Šarić, “A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations,” <i>Soft Matter</i>, vol. 21, no. 40. Royal Society of Chemistry, pp. 7736–7756, 2025.","chicago":"Muñoz Basagoiti, Maitane, Felix F Frey, Billie Meadowcroft, Miguel Santana de Freitas Amaral, Adam Prada, and Anđela Šarić. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>.","apa":"Muñoz Basagoiti, M., Frey, F. F., Meadowcroft, B., Santana de Freitas Amaral, M., Prada, A., &#38; Šarić, A. (2025). A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>","short":"M. Muñoz Basagoiti, F.F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, A. Šarić, Soft Matter 21 (2025) 7736–7756.","ista":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. 2025. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. Soft Matter. 21(40), 7736–7756.","mla":"Muñoz Basagoiti, Maitane, et al. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>, vol. 21, no. 40, Royal Society of Chemistry, 2025, pp. 7736–56, doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>.","ama":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. 2025;21(40):7736-7756. doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>"},"department":[{"_id":"AnSa"}]},{"_id":"21237","date_updated":"2026-02-17T11:27:48Z","article_processing_charge":"No","issue":"21","language":[{"iso":"eng"}],"OA_type":"green","OA_place":"repository","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"apa":"Baulin, V. A., Giacometti, A., Fedosov, D. A., Ebbens, S., Varela-Rosales, N. R., Feliu, N., … Hanczyc, M. M. (2025). Intelligent soft matter: Towards embodied intelligence. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d5sm00174a\">https://doi.org/10.1039/d5sm00174a</a>","ama":"Baulin VA, Giacometti A, Fedosov DA, et al. Intelligent soft matter: Towards embodied intelligence. <i>Soft Matter</i>. 2025;(21):4129-4145. doi:<a href=\"https://doi.org/10.1039/d5sm00174a\">10.1039/d5sm00174a</a>","mla":"Baulin, Vladimir A., et al. “Intelligent Soft Matter: Towards Embodied Intelligence.” <i>Soft Matter</i>, no. 21, Royal Society of Chemistry, 2025, pp. 4129–45, doi:<a href=\"https://doi.org/10.1039/d5sm00174a\">10.1039/d5sm00174a</a>.","ista":"Baulin VA, Giacometti A, Fedosov DA, Ebbens S, Varela-Rosales NR, Feliu N, Chowdhury M, Hu M, Füchslin R, Dijkstra M, Mussel M, van Roij R, Xie D, Tzanov V, Zu M, Hidalgo-Caballero S, Yuan Y, Cocconi L, Ghim C-M, Cottin-Bizonne C, Miguel MC, Esplandiu MJ, Simmchen J, Parak WJ, Werner M, Gompper G, Hanczyc MM. 2025. Intelligent soft matter: Towards embodied intelligence. Soft Matter. (21), 4129–4145.","short":"V.A. Baulin, A. Giacometti, D.A. Fedosov, S. Ebbens, N.R. Varela-Rosales, N. Feliu, M. Chowdhury, M. Hu, R. Füchslin, M. Dijkstra, M. Mussel, R. van Roij, D. Xie, V. Tzanov, M. Zu, S. Hidalgo-Caballero, Y. Yuan, L. Cocconi, C.-M. Ghim, C. Cottin-Bizonne, M.C. Miguel, M.J. Esplandiu, J. Simmchen, W.J. Parak, M. Werner, G. Gompper, M.M. Hanczyc, Soft Matter (2025) 4129–4145.","chicago":"Baulin, Vladimir A., Achille Giacometti, Dmitry A. Fedosov, Stephen Ebbens, Nydia R. Varela-Rosales, Neus Feliu, Mithun Chowdhury, et al. “Intelligent Soft Matter: Towards Embodied Intelligence.” <i>Soft Matter</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d5sm00174a\">https://doi.org/10.1039/d5sm00174a</a>.","ieee":"V. A. Baulin <i>et al.</i>, “Intelligent soft matter: Towards embodied intelligence,” <i>Soft Matter</i>, no. 21. Royal Society of Chemistry, pp. 4129–4145, 2025."},"department":[{"_id":"CaGo"}],"pmid":1,"external_id":{"pmid":["40358970"]},"date_published":"2025-06-07T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","publisher":"Royal Society of Chemistry","acknowledgement":"The work is the result of the SoftComp Topical workshop on Intelligent Soft Matter, Salou 2025 (https://softmat.net/intelligent-soft-matter/) financed by SoftComp Network of Excellence (https://eu-softcomp.net/). Various AI tools were used for preparation of the manuscript: language models Google Gemini 2.0 series and Discovery Engine (https://explore-the-unknown.vercel.app) for literature processing, structuring contributions, finding concept overlaps and summarizing according to procedure explained in https://github.com/vbaulin/IntelliDE/.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Soft Matter","title":"Intelligent soft matter: Towards embodied intelligence","month":"06","article_type":"review","day":"07","page":"4129-4145","author":[{"full_name":"Baulin, Vladimir A.","first_name":"Vladimir A.","last_name":"Baulin"},{"full_name":"Giacometti, Achille","first_name":"Achille","last_name":"Giacometti"},{"last_name":"Fedosov","first_name":"Dmitry A.","full_name":"Fedosov, Dmitry A."},{"first_name":"Stephen","last_name":"Ebbens","full_name":"Ebbens, Stephen"},{"first_name":"Nydia R.","last_name":"Varela-Rosales","full_name":"Varela-Rosales, Nydia R."},{"full_name":"Feliu, Neus","last_name":"Feliu","first_name":"Neus"},{"full_name":"Chowdhury, Mithun","last_name":"Chowdhury","first_name":"Mithun"},{"last_name":"Hu","first_name":"Minghan","full_name":"Hu, Minghan"},{"last_name":"Füchslin","first_name":"Rudolf","full_name":"Füchslin, Rudolf"},{"full_name":"Dijkstra, Marjolein","first_name":"Marjolein","last_name":"Dijkstra"},{"full_name":"Mussel, Matan","last_name":"Mussel","first_name":"Matan"},{"last_name":"van Roij","first_name":"René","full_name":"van Roij, René"},{"full_name":"Xie, Dong","first_name":"Dong","last_name":"Xie"},{"last_name":"Tzanov","first_name":"Vassil","full_name":"Tzanov, Vassil"},{"id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","full_name":"Zu, Mengjie","first_name":"Mengjie","last_name":"Zu"},{"full_name":"Hidalgo-Caballero, Samuel","first_name":"Samuel","last_name":"Hidalgo-Caballero"},{"last_name":"Yuan","first_name":"Ye","full_name":"Yuan, Ye"},{"last_name":"Cocconi","first_name":"Luca","full_name":"Cocconi, Luca"},{"full_name":"Ghim, Cheol-Min","first_name":"Cheol-Min","last_name":"Ghim"},{"last_name":"Cottin-Bizonne","first_name":"Cécile","full_name":"Cottin-Bizonne, Cécile"},{"last_name":"Miguel","first_name":"M. Carmen","full_name":"Miguel, M. Carmen"},{"full_name":"Esplandiu, Maria Jose","first_name":"Maria Jose","last_name":"Esplandiu"},{"first_name":"Juliane","last_name":"Simmchen","full_name":"Simmchen, Juliane"},{"full_name":"Parak, Wolfgang J.","first_name":"Wolfgang J.","last_name":"Parak"},{"last_name":"Werner","first_name":"Marco","full_name":"Werner, Marco"},{"full_name":"Gompper, Gerhard","first_name":"Gerhard","last_name":"Gompper"},{"last_name":"Hanczyc","first_name":"Martin M.","full_name":"Hanczyc, Martin M."}],"doi":"10.1039/d5sm00174a","year":"2025","status":"public","quality_controlled":"1","type":"journal_article","oa":1,"date_created":"2026-02-16T15:03:08Z","abstract":[{"text":"Intelligent soft matter lies at the intersection of materials science, physics, and cognitive science, promising to change how we design and interact with materials. This transformative field aims to create materials with life-like capabilities, such as perception, learning, memory, and adaptive behavior. Unlike traditional materials, which typically perform static or predefined functions, intelligent soft matter can dynamically interact with its environment, integrating multiple sensory inputs, retaining past experiences, and making decisions to optimize its responses. Inspired by biological systems, these materials leverage the inherent properties of soft matter such as flexibility, adaptability, and responsiveness to perform functions that mimic cognitive processes. By synthesizing current research trends and projecting their evolution, we present a forward-looking perspective on how intelligent soft matter could be constructed, with the aim of inspiring innovations in areas such as biomedical devices, adaptive robotics, and beyond. We highlight new pathways for integrating sensing, memory and actuation with low-power internal operations, and we discuss key challenges in realizing materials that exhibit truly “intelligent behavior”. These approaches outline a path toward more robust, versatile, and scalable materials that can potentially act, compute, and “think” through their inherent intrinsic material properties—moving beyond traditional smart technologies that rely on external control.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprints.whiterose.ac.uk/id/eprint/226553/4/Perspective_v6_clean.pdf"}]},{"quality_controlled":"1","arxiv":1,"status":"public","oa":1,"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","date_updated":"2024-01-30T12:48:24Z","checksum":"b936747170d0b708172b518078c4081a","file_size":7660662,"file_id":"14908","file_name":"2023_SoftMatter_Ronning.pdf","date_created":"2024-01-30T12:48:24Z","content_type":"application/pdf","success":1}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2023-08-20T22:01:15Z","month":"09","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","ddc":["540"],"article_type":"original","year":"2023","doi":"10.1039/d3sm00316g","author":[{"last_name":"Rønning","first_name":"Jonas","full_name":"Rønning, Jonas"},{"first_name":"Julian B","last_name":"Renaud","full_name":"Renaud, Julian B","id":"7af6767d-14eb-11ed-b536-a32449ae867c"},{"last_name":"Doostmohammadi","first_name":"Amin","full_name":"Doostmohammadi, Amin"},{"last_name":"Angheluta","first_name":"Luiza","full_name":"Angheluta, Luiza"}],"scopus_import":"1","page":"7513-7527","day":"01","oa_version":"Published Version","date_published":"2023-09-01T00:00:00Z","volume":39,"publisher":"Royal Society of Chemistry","publication_status":"published","isi":1,"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.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"license":"https://creativecommons.org/licenses/by/4.0/","publication":"Soft Matter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        39","file_date_updated":"2024-01-30T12:48:24Z","article_processing_charge":"Yes (in subscription journal)","date_updated":"2025-04-23T13:03:12Z","_id":"14087","has_accepted_license":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["37493084"],"arxiv":["2303.07063"],"isi":["001035766100001"]},"pmid":1,"department":[{"_id":"GradSch"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"ieee":"J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” <i>Soft Matter</i>, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.","chicago":"Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>.","apa":"Rønning, J., Renaud, J. B., Doostmohammadi, A., &#38; Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>","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.","short":"J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527.","mla":"Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>.","ama":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. 2023;39:7513-7527. doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>"}},{"ec_funded":1,"oa_version":"Published Version","date_published":"2023-02-06T00:00:00Z","volume":19,"publication_status":"published","publisher":"Royal Society of Chemistry","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).","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"Soft Matter","intvolume":"        19","file_date_updated":"2023-03-07T09:19:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-23T08:48:51Z","article_processing_charge":"No","_id":"12708","language":[{"iso":"eng"}],"has_accepted_license":"1","external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"],"pmid":["36779972"]},"citation":{"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. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>","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.","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.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>.","ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","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.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"department":[{"_id":"AnSa"}],"pmid":1,"quality_controlled":"1","arxiv":1,"status":"public","oa":1,"file":[{"file_name":"2023_SoftMatter_Araujo.pdf","date_created":"2023-03-07T09:19:41Z","content_type":"application/pdf","success":1,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_size":3581939,"file_id":"12711","relation":"main_file","creator":"cchlebak","access_level":"open_access","date_updated":"2023-03-07T09:19:41Z"}],"type":"journal_article","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."}],"date_created":"2023-03-05T23:01:06Z","month":"02","title":"Steering self-organisation through confinement","ddc":["540"],"article_type":"original","project":[{"call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"author":[{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"full_name":"Barois, Thomas","last_name":"Barois","first_name":"Thomas"},{"full_name":"Boffetta, Guido","last_name":"Boffetta","first_name":"Guido"},{"last_name":"Cohen","first_name":"Itai","full_name":"Cohen, Itai"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"full_name":"Dauchot, Olivier","first_name":"Olivier","last_name":"Dauchot"},{"first_name":"Marjolein","last_name":"Dijkstra","full_name":"Dijkstra, Marjolein"},{"last_name":"Durham","first_name":"William M.","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","first_name":"Audrey","last_name":"Dussutour"},{"full_name":"Garnier, Simon","first_name":"Simon","last_name":"Garnier"},{"full_name":"Gelderblom, Hanneke","first_name":"Hanneke","last_name":"Gelderblom"},{"first_name":"Ramin","last_name":"Golestanian","full_name":"Golestanian, Ramin"},{"full_name":"Isa, Lucio","last_name":"Isa","first_name":"Lucio"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"full_name":"Löwen, Hartmut","first_name":"Hartmut","last_name":"Löwen"},{"full_name":"Metzler, Ralf","first_name":"Ralf","last_name":"Metzler"},{"first_name":"Marco","last_name":"Polin","full_name":"Polin, Marco"},{"full_name":"Royall, C. Patrick","first_name":"C. Patrick","last_name":"Royall"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Sengupta","first_name":"Anupam","full_name":"Sengupta, Anupam"},{"last_name":"Sykes","first_name":"Cécile","full_name":"Sykes, Cécile"},{"last_name":"Trianni","first_name":"Vito","full_name":"Trianni, Vito"},{"first_name":"Idan","last_name":"Tuval","full_name":"Tuval, Idan"},{"full_name":"Vogel, Nicolas","last_name":"Vogel","first_name":"Nicolas"},{"full_name":"Yeomans, Julia M.","first_name":"Julia M.","last_name":"Yeomans"},{"last_name":"Zuriguel","first_name":"Iker","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","first_name":"Alvaro","last_name":"Marin"},{"full_name":"Volpe, Giorgio","first_name":"Giorgio","last_name":"Volpe"}],"doi":"10.1039/d2sm01562e","year":"2023","day":"06","page":"1695-1704","scopus_import":"1"},{"scopus_import":"1","page":"9107-9115","day":"20","doi":"10.1039/d1sm00774b","year":"2021","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":"Mathematics, Computer Science"}],"author":[{"orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Saadatfar","first_name":"Mohammad","full_name":"Saadatfar, Mohammad"}],"article_type":"original","ddc":["540"],"title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","month":"10","date_created":"2021-10-31T23:01:30Z","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."}],"type":"journal_article","oa":1,"file":[{"file_id":"14385","file_size":4678788,"checksum":"b4da0c420530295e61b153960f6cb350","date_updated":"2023-10-03T09:21:42Z","access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2023-10-03T09:21:42Z","file_name":"2021_SoftMatter_acceptedversion_Osang.pdf"}],"status":"public","quality_controlled":"1","pmid":1,"department":[{"_id":"HeEd"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>. Royal Society of Chemistry , 2021. <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>.","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” <i>Soft Matter</i>, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","apa":"Osang, G. F., Edelsbrunner, H., &#38; Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. 2021;17(40):9107-9115. doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>.","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.","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115."},"external_id":{"isi":["000700090000001"],"pmid":["34569592"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"issue":"40","_id":"10204","article_processing_charge":"No","date_updated":"2025-04-15T07:16:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-10-03T09:21:42Z","intvolume":"        17","publication":"Soft Matter","isi":1,"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.","publisher":"Royal Society of Chemistry ","publication_status":"published","date_published":"2021-10-20T00:00:00Z","volume":17,"oa_version":"Submitted Version","ec_funded":1},{"author":[{"last_name":"Vanhille-Campos","first_name":"Christian","full_name":"Vanhille-Campos, Christian"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"}],"doi":"10.1039/d0sm02012e","year":"2021","day":"16","page":"3798-3806","scopus_import":"1","article_type":"original","related_material":{"link":[{"relation":"earlier_version","url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2"}]},"month":"02","title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","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."}],"main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e"}],"date_created":"2021-11-25T16:06:42Z","keyword":["condensed matter physics","general chemistry"],"oa":1,"type":"journal_article","quality_controlled":"1","status":"public","external_id":{"pmid":["33629089"]},"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” <i>Soft Matter</i>, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>.","apa":"Vanhille-Campos, C., &#38; Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>","short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","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.” <i>Soft Matter</i>, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>.","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. 2021;17(14):3798-3806. doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>"},"pmid":1,"OA_place":"publisher","language":[{"iso":"eng"}],"OA_type":"hybrid","extern":"1","issue":"14","date_updated":"2024-10-14T14:20:59Z","article_processing_charge":"No","_id":"10339","publication":"Soft Matter","license":"https://creativecommons.org/licenses/by-nc/3.0/","intvolume":"        17","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","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.","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)"},"publication_status":"published","publisher":"Royal Society of Chemistry","oa_version":"Published Version","volume":17,"date_published":"2021-02-16T00:00:00Z"},{"date_published":"2020-10-06T00:00:00Z","volume":16,"oa_version":"Published Version","publication_status":"published","publisher":"Royal Society of Chemistry","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.).","intvolume":"        16","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","publication":"Soft Matter","_id":"10341","date_updated":"2024-10-16T12:53:17Z","article_processing_charge":"No","issue":"47","extern":"1","OA_place":"publisher","language":[{"iso":"eng"}],"OA_type":"hybrid","publication_identifier":{"issn":["1744-683X","1744-6848"]},"citation":{"apa":"Debets, V. E., Janssen, L. M. C., &#38; Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>","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.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. 2020;16(47):10628-10639. doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” <i>Soft Matter</i>, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>."},"pmid":1,"external_id":{"pmid":["33084724"]},"status":"public","quality_controlled":"1","type":"journal_article","keyword":["condensed matter physics","general chemistry"],"oa":1,"date_created":"2021-11-26T06:29:41Z","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."}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1"}],"title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","month":"10","article_type":"original","day":"06","page":"10628-10639","scopus_import":"1","author":[{"first_name":"V. E.","last_name":"Debets","full_name":"Debets, V. E."},{"last_name":"Janssen","first_name":"L. M. C.","full_name":"Janssen, L. M. C."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"doi":"10.1039/d0sm00712a","year":"2020"},{"intvolume":"        16","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication":"Soft Matter","volume":16,"date_published":"2020-05-07T00:00:00Z","oa_version":"None","publication_status":"published","publisher":"Royal Society of Chemistry ","extern":"1","language":[{"iso":"eng"}],"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. <i>Soft Matter</i>. 2020;16(17):4274-4282. doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>","mla":"Youssef, Mena, et al. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” <i>Soft Matter</i>, vol. 16, no. 17, Royal Society of Chemistry , 2020, pp. 4274–82, doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>.","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.","short":"M. Youssef, A. Morin, A. Aubret, S. Sacanna, J.A. Palacci, Soft Matter 16 (2020) 4274–4282.","apa":"Youssef, M., Morin, A., Aubret, A., Sacanna, S., &#38; Palacci, J. A. (2020). Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>","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.” <i>Soft Matter</i>. Royal Society of Chemistry , 2020. <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>.","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,” <i>Soft Matter</i>, vol. 16, no. 17. Royal Society of Chemistry , pp. 4274–4282, 2020."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"pmid":1,"external_id":{"pmid":["32307507"]},"_id":"9054","date_updated":"2023-02-23T13:47:45Z","article_processing_charge":"No","issue":"17","type":"journal_article","keyword":["General Chemistry","Condensed Matter Physics"],"date_created":"2021-02-01T13:45:11Z","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."}],"status":"public","quality_controlled":"1","article_type":"original","day":"07","scopus_import":"1","page":"4274-4282","author":[{"full_name":"Youssef, Mena","last_name":"Youssef","first_name":"Mena"},{"full_name":"Morin, Alexandre","first_name":"Alexandre","last_name":"Morin"},{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"doi":"10.1039/c9sm01850f","year":"2020","title":"Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt","month":"05"},{"publisher":"Royal Society of Chemistry","publication_status":"published","volume":15,"date_published":"2019-01-10T00:00:00Z","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-10-09T11:00:05Z","intvolume":"        15","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","publication":"Soft Matter","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"isi":1,"issue":"4","_id":"5817","article_processing_charge":"No","date_updated":"2024-10-09T20:58:29Z","department":[{"_id":"GaTk"}],"pmid":1,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” <i>Soft Matter</i>, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., &#38; Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. 2019;15(4):602-614. doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>."},"external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"corr_author":"1","status":"public","quality_controlled":"1","date_created":"2019-01-11T07:37:47Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2020-10-09T11:00:05Z","content_type":"application/pdf","file_name":"lmt_sftmtr_V8.pdf","success":1,"file_size":5370762,"checksum":"614c337d6424ccd3d48d1b1f9513510d","file_id":"8641","relation":"main_file","date_updated":"2020-10-09T11:00:05Z","creator":"bkavcic","access_level":"open_access"}],"oa":1,"ddc":["530"],"title":"Limiting shapes of confined lipid vesicles","month":"01","scopus_import":"1","page":"602-614","day":"10","year":"2019","doi":"10.1039/c8sm01956h","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X"},{"last_name":"Sakashita","first_name":"A.","full_name":"Sakashita, A."},{"last_name":"Noguchi","first_name":"H.","full_name":"Noguchi, H."},{"full_name":"Ziherl, P.","last_name":"Ziherl","first_name":"P."}],"article_type":"original"},{"article_type":"original","day":"15","scopus_import":"1","page":"5804-5809","author":[{"last_name":"Khattak","first_name":"Hamza K.","full_name":"Khattak, Hamza K."},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Slepkov, Aaron D.","first_name":"Aaron D.","last_name":"Slepkov"}],"doi":"10.1039/c9sm00756c","year":"2019","title":"Microwave induced mechanical activation of hydrogel dimers","month":"07","type":"journal_article","date_created":"2019-08-04T21:59:21Z","abstract":[{"lang":"eng","text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics."}],"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"apa":"Khattak, H. K., Waitukaitis, S. R., &#38; Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>","mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>.","ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. 2019;15(29):5804-5809. doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>.","ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” <i>Soft Matter</i>, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019."},"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"pmid":1,"department":[{"_id":"ScWa"}],"external_id":{"isi":["000476909200002"],"pmid":["31305853"]},"_id":"6763","date_updated":"2025-07-10T11:53:49Z","article_processing_charge":"No","issue":"29","isi":1,"intvolume":"        15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Soft Matter","date_published":"2019-07-15T00:00:00Z","volume":15,"oa_version":"None","publication_status":"published","publisher":"Royal Society of Chemistry"},{"article_type":"original","year":"2018","doi":"10.1039/c8sm01760c","author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465"}],"scopus_import":"1","page":"9577-9588","day":"21","month":"12","title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","oa":1,"keyword":["General Chemistry","Condensed Matter Physics"],"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1909.11121","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"date_created":"2021-02-01T13:44:41Z","arxiv":1,"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"extern":"1","external_id":{"arxiv":["1909.11121"],"pmid":["30456407"]},"pmid":1,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"apa":"Aubret, A., &#38; Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588.","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.” <i>Soft Matter</i>, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>.","ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. 2018;14(47):9577-9588. doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” <i>Soft Matter</i>, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018.","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>. Royal Society of Chemistry , 2018. <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>."},"article_processing_charge":"No","date_updated":"2023-02-23T13:47:43Z","_id":"9053","issue":"47","publication":"Soft Matter","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":"        14","oa_version":"Preprint","volume":14,"date_published":"2018-12-21T00:00:00Z","publisher":"Royal Society of Chemistry ","publication_status":"published"},{"extern":"1","language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"citation":{"chicago":"Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/c7sm00433h\">https://doi.org/10.1039/c7sm00433h</a>.","ieee":"A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” <i>Soft Matter</i>, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017.","ama":"Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. <i>Soft Matter</i>. 2017;13(28):4924-4930. doi:<a href=\"https://doi.org/10.1039/c7sm00433h\">10.1039/c7sm00433h</a>","mla":"Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” <i>Soft Matter</i>, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:<a href=\"https://doi.org/10.1039/c7sm00433h\">10.1039/c7sm00433h</a>.","short":"A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.","ista":"Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930.","apa":"Vahid, A., Šarić, A., &#38; Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c7sm00433h\">https://doi.org/10.1039/c7sm00433h</a>"},"external_id":{"pmid":["28677712"],"arxiv":["1703.00776"]},"_id":"10375","article_processing_charge":"No","date_updated":"2021-11-29T10:33:36Z","issue":"28","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        13","license":"https://creativecommons.org/licenses/by/3.0/","publication":"Soft Matter","date_published":"2017-06-15T00:00:00Z","volume":13,"oa_version":"Published Version","publisher":"Royal Society of Chemistry","publication_status":"published","article_type":"original","scopus_import":"1","page":"4924-4930","day":"15","year":"2017","doi":"10.1039/c7sm00433h","author":[{"first_name":"Afshin","last_name":"Vahid","full_name":"Vahid, Afshin"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"}],"title":"Curvature variation controls particle aggregation on fluid vesicles","month":"06","type":"journal_article","oa":1,"keyword":["condensed matter physics","general chemistry"],"date_created":"2021-11-29T10:00:39Z","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H"}],"abstract":[{"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.","lang":"eng"}],"status":"public","quality_controlled":"1","arxiv":1},{"article_type":"original","author":[{"full_name":"Bachmann, Stephan Jan","last_name":"Bachmann","first_name":"Stephan Jan"},{"full_name":"Kotar, Jurij","first_name":"Jurij","last_name":"Kotar"},{"full_name":"Parolini, Lucia","last_name":"Parolini","first_name":"Lucia"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Cicuta, Pietro","last_name":"Cicuta","first_name":"Pietro"},{"full_name":"Di Michele, Lorenzo","last_name":"Di Michele","first_name":"Lorenzo"},{"last_name":"Mognetti","first_name":"Bortolo Matteo","full_name":"Mognetti, Bortolo Matteo"}],"doi":"10.1039/c6sm01515h","year":"2016","day":"19","scopus_import":"1","page":"7804-7817","month":"08","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","keyword":["condensed matter physics","general chemistry"],"oa":1,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05788"}],"date_created":"2021-11-29T11:09:55Z","arxiv":1,"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"extern":"1","external_id":{"arxiv":["1608.05788"],"pmid":["27722701"]},"citation":{"ieee":"S. J. Bachmann <i>et al.</i>, “Melting transition in lipid vesicles functionalised by mobile DNA linkers,” <i>Soft Matter</i>, vol. 12, no. 37. Royal Society of Chemistry, pp. 7804–7817, 2016.","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.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>.","apa":"Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., &#38; Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>","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.","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>.","ama":"Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. 2016;12(37):7804-7817. doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>"},"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"pmid":1,"date_updated":"2021-11-29T13:09:00Z","article_processing_charge":"No","_id":"10381","issue":"37","publication":"Soft Matter","intvolume":"        12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","date_published":"2016-08-19T00:00:00Z","volume":12,"publication_status":"published","publisher":"Royal Society of Chemistry"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:40:56Z","intvolume":"        12","publication":"Soft Matter","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."}],"type":"journal_article","publisher":"Royal Society of Chemistry","publication_status":"published","status":"public","date_published":"2016-03-14T00:00:00Z","volume":12,"oa_version":"None","quality_controlled":"1","page":"3982-3990","day":"14","citation":{"chicago":"Sussman, Daniel M., Carl Peter Goodrich, and Andrea J. Liu. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>.","ieee":"D. M. Sussman, C. P. Goodrich, and A. J. Liu, “Spatial structure of states of self stress in jammed systems,” <i>Soft Matter</i>, vol. 12, no. 17. Royal Society of Chemistry, pp. 3982–3990, 2016.","mla":"Sussman, Daniel M., et al. “Spatial Structure of States of Self Stress in Jammed Systems.” <i>Soft Matter</i>, vol. 12, no. 17, Royal Society of Chemistry, 2016, pp. 3982–90, doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>.","ama":"Sussman DM, Goodrich CP, Liu AJ. Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. 2016;12(17):3982-3990. doi:<a href=\"https://doi.org/10.1039/c6sm00094k\">10.1039/c6sm00094k</a>","ista":"Sussman DM, Goodrich CP, Liu AJ. 2016. Spatial structure of states of self stress in jammed systems. Soft Matter. 12(17), 3982–3990.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, Soft Matter 12 (2016) 3982–3990.","apa":"Sussman, D. M., Goodrich, C. P., &#38; Liu, A. J. (2016). Spatial structure of states of self stress in jammed systems. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm00094k\">https://doi.org/10.1039/c6sm00094k</a>"},"publication_identifier":{"issn":["1744-683X","1744-6848"]},"doi":"10.1039/c6sm00094k","year":"2016","author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."}],"extern":"1","article_type":"original","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://doi.org/10.1039/c6sm02496c","relation":"other"}]},"issue":"17","title":"Spatial structure of states of self stress in jammed systems","_id":"7764","article_processing_charge":"No","month":"03","date_updated":"2021-01-12T08:15:22Z"},{"extern":"1","language":[{"iso":"eng"}],"pmid":1,"citation":{"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.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c5sm03127c\">https://doi.org/10.1039/c5sm03127c</a>.","ieee":"M. S. Davies Wykes <i>et al.</i>, “Dynamic self-assembly of microscale rotors and swimmers,” <i>Soft Matter</i>, vol. 12, no. 20. Royal Society of Chemistry, pp. 4584–4589, 2016.","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. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5sm03127c\">https://doi.org/10.1039/c5sm03127c</a>","mla":"Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” <i>Soft Matter</i>, vol. 12, no. 20, Royal Society of Chemistry, 2016, pp. 4584–89, doi:<a href=\"https://doi.org/10.1039/c5sm03127c\">10.1039/c5sm03127c</a>.","ama":"Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale rotors and swimmers. <i>Soft Matter</i>. 2016;12(20):4584-4589. doi:<a href=\"https://doi.org/10.1039/c5sm03127c\">10.1039/c5sm03127c</a>","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.","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."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"external_id":{"pmid":["27121100"],"arxiv":["1509.06330"]},"_id":"9051","article_processing_charge":"No","date_updated":"2023-02-23T13:47:38Z","issue":"20","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":"        12","publication":"Soft Matter","volume":12,"date_published":"2016-05-28T00:00:00Z","oa_version":"Preprint","publisher":"Royal Society of Chemistry","publication_status":"published","article_type":"original","page":"4584-4589","scopus_import":"1","day":"28","doi":"10.1039/c5sm03127c","year":"2016","author":[{"last_name":"Davies Wykes","first_name":"Megan S.","full_name":"Davies Wykes, Megan S."},{"first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"last_name":"Adachi","first_name":"Takuji","full_name":"Adachi, Takuji"},{"first_name":"Leif","last_name":"Ristroph","full_name":"Ristroph, Leif"},{"last_name":"Zhong","first_name":"Xiao","full_name":"Zhong, Xiao"},{"full_name":"Ward, Michael D.","last_name":"Ward","first_name":"Michael D."},{"last_name":"Zhang","first_name":"Jun","full_name":"Zhang, Jun"},{"first_name":"Michael J.","last_name":"Shelley","full_name":"Shelley, Michael J."}],"title":"Dynamic self-assembly of microscale rotors and swimmers","month":"05","type":"journal_article","oa":1,"date_created":"2021-02-01T13:44:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1509.06330","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"status":"public","quality_controlled":"1","arxiv":1},{"status":"public","arxiv":1,"quality_controlled":"1","type":"journal_article","keyword":["General Chemistry","Condensed Matter Physics"],"oa":1,"date_created":"2021-02-01T13:44:15Z","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1609.01497","open_access":"1"}],"title":"Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam","month":"08","article_type":"original","day":"14","page":"6357-6364","scopus_import":"1","author":[{"first_name":"Henrique","last_name":"Moyses","full_name":"Moyses, Henrique"},{"first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"last_name":"Grier","first_name":"David G.","full_name":"Grier, David G."}],"doi":"10.1039/c6sm01163b","year":"2016","volume":12,"date_published":"2016-08-14T00:00:00Z","oa_version":"Preprint","publication_status":"published","publisher":"Royal Society of Chemistry ","intvolume":"        12","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication":"Soft Matter","_id":"9052","date_updated":"2023-02-23T13:47:40Z","article_processing_charge":"No","issue":"30","extern":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"apa":"Moyses, H., Palacci, J. A., Sacanna, S., &#38; Grier, D. G. (2016). Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c6sm01163b\">https://doi.org/10.1039/c6sm01163b</a>","mla":"Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” <i>Soft Matter</i>, vol. 12, no. 30, Royal Society of Chemistry , 2016, pp. 6357–64, doi:<a href=\"https://doi.org/10.1039/c6sm01163b\">10.1039/c6sm01163b</a>.","ama":"Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. <i>Soft Matter</i>. 2016;12(30):6357-6364. doi:<a href=\"https://doi.org/10.1039/c6sm01163b\">10.1039/c6sm01163b</a>","short":"H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364.","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.","chicago":"Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” <i>Soft Matter</i>. Royal Society of Chemistry , 2016. <a href=\"https://doi.org/10.1039/c6sm01163b\">https://doi.org/10.1039/c6sm01163b</a>.","ieee":"H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam,” <i>Soft Matter</i>, vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016."},"pmid":1,"external_id":{"pmid":["27338294"],"arxiv":["1609.01497"]}},{"article_type":"original","extern":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1744-683X","1744-6848"]},"citation":{"ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” <i>Soft Matter</i>, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” <i>Soft Matter</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c4sm02905d\">https://doi.org/10.1039/c4sm02905d</a>.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c4sm02905d\">https://doi.org/10.1039/c4sm02905d</a>","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. <i>Soft Matter</i>. 2015;11(14):2745-2751. doi:<a href=\"https://doi.org/10.1039/c4sm02905d\">10.1039/c4sm02905d</a>","mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” <i>Soft Matter</i>, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:<a href=\"https://doi.org/10.1039/c4sm02905d\">10.1039/c4sm02905d</a>."},"day":"15","page":"2745-2751","author":[{"full_name":"Sussman, Daniel M.","last_name":"Sussman","first_name":"Daniel M."},{"first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"doi":"10.1039/c4sm02905d","year":"2015","_id":"7766","title":"Disordered surface vibrations in jammed sphere packings","date_updated":"2021-01-12T08:15:23Z","article_processing_charge":"No","month":"02","issue":"14","type":"journal_article","date_created":"2020-04-30T11:41:23Z","intvolume":"        11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"publication":"Soft Matter","volume":11,"status":"public","date_published":"2015-02-15T00:00:00Z","quality_controlled":"1","oa_version":"None","publication_status":"published","publisher":"Royal Society of Chemistry"},{"author":[{"full_name":"Takagi, Daisuke","first_name":"Daisuke","last_name":"Takagi"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465"},{"full_name":"Braunschweig, Adam B.","last_name":"Braunschweig","first_name":"Adam B."},{"last_name":"Shelley","first_name":"Michael J.","full_name":"Shelley, Michael J."},{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"}],"doi":"10.1039/c3sm52815d","year":"2014","day":"21","scopus_import":"1","article_number":"1784","article_type":"original","month":"03","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.5662"}],"date_created":"2021-02-01T13:43:31Z","keyword":["General Chemistry","Condensed Matter Physics"],"oa":1,"type":"journal_article","arxiv":1,"quality_controlled":"1","status":"public","external_id":{"pmid":["24800268"],"arxiv":["1309.5662"]},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","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.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>"},"pmid":1,"language":[{"iso":"eng"}],"extern":"1","issue":"11","date_updated":"2023-02-23T13:47:35Z","article_processing_charge":"No","_id":"9050","publication":"Soft Matter","intvolume":"        10","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_status":"published","publisher":"Royal Society of Chemistry ","oa_version":"Preprint","volume":10,"date_published":"2014-03-21T00:00:00Z"},{"acknowledgement":"This work was supported by the National Science Foundation under Career Grant no. DMR-0846426.","publication":"Soft Matter","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"         9","oa_version":"None","date_published":"2013-08-08T00:00:00Z","volume":9,"publisher":"Royal Society of Chemistry","publication_status":"published","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"chicago":"Napoli, Joseph A., Anđela Šarić, and Angelo Cacciuto. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>.","ieee":"J. A. Napoli, A. Šarić, and A. Cacciuto, “Collapsing nanoparticle-laden nanotubes,” <i>Soft Matter</i>, vol. 9, no. 37. Royal Society of Chemistry, pp. 8881–8886, 2013.","ama":"Napoli JA, Šarić A, Cacciuto A. Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. 2013;9(37):8881-8886. doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>","mla":"Napoli, Joseph A., et al. “Collapsing Nanoparticle-Laden Nanotubes.” <i>Soft Matter</i>, vol. 9, no. 37, Royal Society of Chemistry, 2013, pp. 8881–86, doi:<a href=\"https://doi.org/10.1039/c3sm51495a\">10.1039/c3sm51495a</a>.","short":"J.A. Napoli, A. Šarić, A. Cacciuto, Soft Matter 9 (2013) 8881–8886.","ista":"Napoli JA, Šarić A, Cacciuto A. 2013. Collapsing nanoparticle-laden nanotubes. Soft Matter. 9(37), 8881–8886.","apa":"Napoli, J. A., Šarić, A., &#38; Cacciuto, A. (2013). Collapsing nanoparticle-laden nanotubes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm51495a\">https://doi.org/10.1039/c3sm51495a</a>"},"article_processing_charge":"No","date_updated":"2021-11-29T14:05:23Z","_id":"10385","issue":"37","keyword":["condensed matter physics","general chemistry"],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2021-11-29T13:31:24Z","quality_controlled":"1","status":"public","article_type":"original","doi":"10.1039/c3sm51495a","year":"2013","author":[{"full_name":"Napoli, Joseph A.","first_name":"Joseph A.","last_name":"Napoli"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"page":"8881-8886","scopus_import":"1","day":"08","month":"08","title":"Collapsing nanoparticle-laden nanotubes"},{"article_number":"6677","article_type":"original","author":[{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"year":"2013","doi":"10.1039/c3sm50188d","day":"03","scopus_import":"1","month":"05","title":"Self-assembly of nanoparticles adsorbed on fluid and elastic membranes","keyword":["condensed matter physics","general chemistry"],"type":"journal_article","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."}],"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2013/sm/c3sm50188d"}],"date_created":"2021-11-29T14:06:32Z","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"extern":"1","citation":{"ama":"Šarić A, Cacciuto A. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. 2013;9(29). doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>, vol. 9, no. 29, 6677, Royal Society of Chemistry, 2013, doi:<a href=\"https://doi.org/10.1039/c3sm50188d\">10.1039/c3sm50188d</a>.","short":"A. Šarić, A. Cacciuto, Soft Matter 9 (2013).","ista":"Šarić A, Cacciuto A. 2013. Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. Soft Matter. 9(29), 6677.","apa":"Šarić, A., &#38; Cacciuto, A. (2013). Self-assembly of nanoparticles adsorbed on fluid and elastic membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Self-Assembly of Nanoparticles Adsorbed on Fluid and Elastic Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2013. <a href=\"https://doi.org/10.1039/c3sm50188d\">https://doi.org/10.1039/c3sm50188d</a>.","ieee":"A. Šarić and A. Cacciuto, “Self-assembly of nanoparticles adsorbed on fluid and elastic membranes,” <i>Soft Matter</i>, vol. 9, no. 29. Royal Society of Chemistry, 2013."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"date_updated":"2021-11-29T14:29:31Z","article_processing_charge":"No","_id":"10386","issue":"29","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.","publication":"Soft Matter","intvolume":"         9","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","volume":9,"date_published":"2013-05-03T00:00:00Z","publication_status":"published","publisher":"Royal Society of Chemistry"}]