--- _id: '10135' abstract: - lang: eng text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hana full_name: Semerádová, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semerádová citation: ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135 apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135 chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135. ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021. ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135. short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021. date_created: 2021-10-13T13:42:48Z date_published: 2021-10-13T00:00:00Z date_updated: 2024-01-25T10:53:29Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10135 file: - access_level: closed checksum: ce7108853e6cec6224f17cd6429b51fe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cziletti date_created: 2021-10-27T07:45:37Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10186' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx file_size: 28508629 relation: source_file - access_level: open_access checksum: 0d7afb846e8e31ec794de47bf44e12ef content_type: application/pdf creator: cziletti date_created: 2021-10-27T07:45:57Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-10-28 file_id: '10187' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf file_size: 10623525 relation: main_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. publication_identifier: isbn: - 978-3-99078-014-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9728' abstract: - lang: eng text: "Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nishchal full_name: Agrawal, Nishchal id: 469E6004-F248-11E8-B48F-1D18A9856A87 last_name: Agrawal citation: ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728 apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728 chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728. ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021. ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728. short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021. date_created: 2021-07-27T13:40:30Z date_published: 2021-07-29T00:00:00Z date_updated: 2024-02-28T13:14:39Z day: '29' ddc: - '532' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:9728 file: - access_level: closed checksum: 77436be3563a90435024307b1b5ee7e8 content_type: application/x-zip-compressed creator: nagrawal date_created: 2021-07-28T13:32:02Z date_updated: 2022-07-29T22:30:05Z embargo_to: open_access file_id: '9744' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip file_size: 22859658 relation: source_file - access_level: open_access checksum: 72a891d7daba85445c29b868c22575ed content_type: application/pdf creator: nagrawal date_created: 2021-07-28T13:32:05Z date_updated: 2022-07-29T22:30:05Z embargo: 2022-07-28 file_id: '9745' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf file_size: 18658048 relation: main_file file_date_updated: 2022-07-29T22:30:05Z has_accepted_license: '1' keyword: - Drag Reduction - Transition to Turbulence - Multiphase Flows - particle Laden Flows - Complex Flows - Experiments - Fluid Dynamics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '118' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6189' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Transition to turbulence and drag reduction in particle-laden pipe flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '10336' abstract: - lang: eng text: Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context. acknowledgement: We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1. article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 2020;117(52):33090-33098. doi:10.1073/pnas.2007694117 apa: Krausser, J., Knowles, T. P. J., & Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2007694117 chicago: Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2007694117. ieee: J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” Proceedings of the National Academy of Sciences, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020. ista: Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098. mla: Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” Proceedings of the National Academy of Sciences, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:10.1073/pnas.2007694117. short: J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098. date_created: 2021-11-25T15:07:09Z date_published: 2020-12-16T00:00:00Z date_updated: 2021-11-25T15:35:58Z day: '16' doi: 10.1073/pnas.2007694117 extern: '1' external_id: pmid: - '33328273' intvolume: ' 117' issue: '52' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2 month: '12' oa: 1 oa_version: Published Version page: 33090-33098 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Physical mechanisms of amyloid nucleation on fluid membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 117 year: '2020' ... --- _id: '10342' abstract: - lang: eng text: The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across. acknowledgement: 'Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.' article_number: 'eabc4397 ' article_processing_charge: No article_type: original author: - first_name: Xiaohe full_name: Tian, Xiaohe last_name: Tian - first_name: Diana M. full_name: Leite, Diana M. last_name: Leite - first_name: Edoardo full_name: Scarpa, Edoardo last_name: Scarpa - first_name: Sophie full_name: Nyberg, Sophie last_name: Nyberg - first_name: Gavin full_name: Fullstone, Gavin last_name: Fullstone - first_name: Joe full_name: Forth, Joe last_name: Forth - first_name: Diana full_name: Matias, Diana last_name: Matias - first_name: Azzurra full_name: Apriceno, Azzurra last_name: Apriceno - first_name: Alessandro full_name: Poma, Alessandro last_name: Poma - first_name: Aroa full_name: Duro-Castano, Aroa last_name: Duro-Castano - first_name: Manish full_name: Vuyyuru, Manish last_name: Vuyyuru - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Zhongping full_name: Zhang, Zhongping last_name: Zhang - first_name: Pan full_name: Xiang, Pan last_name: Xiang - first_name: Bin full_name: Fang, Bin last_name: Fang - first_name: Yupeng full_name: Tian, Yupeng last_name: Tian - first_name: Lei full_name: Luo, Lei last_name: Luo - first_name: Loris full_name: Rizzello, Loris last_name: Rizzello - first_name: Giuseppe full_name: Battaglia, Giuseppe last_name: Battaglia citation: ama: 'Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 2020;6(48). doi:10.1126/sciadv.abc4397' apa: 'Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abc4397' chicago: 'Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.abc4397.' ieee: 'X. Tian et al., “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” Science Advances, vol. 6, no. 48. American Association for the Advancement of Science, 2020.' ista: 'Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.' mla: 'Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” Science Advances, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.abc4397.' short: X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020). date_created: 2021-11-26T06:40:28Z date_published: 2020-11-27T00:00:00Z date_updated: 2021-11-26T07:00:24Z day: '27' ddc: - '611' doi: 10.1126/sciadv.abc4397 extern: '1' external_id: pmid: - '33246953' file: - access_level: open_access checksum: 3ba2eca975930cdb0b1ce1ae876885a7 content_type: application/pdf creator: cchlebak date_created: 2021-11-26T06:50:09Z date_updated: 2021-11-26T06:50:09Z file_id: '10343' file_name: 2020_SciAdv_Tian.pdf file_size: 10381298 relation: main_file success: 1 file_date_updated: 2021-11-26T06:50:09Z has_accepted_license: '1' intvolume: ' 6' issue: '48' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: 'On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2020' ... --- _id: '10344' abstract: - lang: eng text: In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry. acknowledgement: We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1). article_number: '228101' article_processing_charge: No article_type: original author: - first_name: Joel C. full_name: Forster, Joel C. last_name: Forster - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Manish R. full_name: Vuyyuru, Manish R. last_name: Vuyyuru - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 2020;125(22). doi:10.1103/physrevlett.125.228101 apa: Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., & Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.228101 chicago: Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.228101. ieee: J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” Physical Review Letters, vol. 125, no. 22. American Physical Society, 2020. ista: Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101. mla: Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” Physical Review Letters, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:10.1103/physrevlett.125.228101. short: J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020). date_created: 2021-11-26T07:10:43Z date_published: 2020-11-23T00:00:00Z date_updated: 2021-11-30T08:33:14Z day: '23' ddc: - '530' doi: 10.1103/physrevlett.125.228101 extern: '1' external_id: pmid: - '33315453' file: - access_level: open_access checksum: fbf2e1415e332d6add90222d60401a1d content_type: application/pdf creator: cchlebak date_created: 2021-11-26T07:16:49Z date_updated: 2021-11-26T07:16:49Z file_id: '10345' file_name: 2020_PhysRevLett_Forster.pdf file_size: 844353 relation: main_file success: 1 file_date_updated: 2021-11-26T07:16:49Z has_accepted_license: '1' intvolume: ' 125' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Exploring the design rules for efficient membrane-reshaping nanostructures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 125 year: '2020' ...