1
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Liu H, Matthies M, Russo J, Rovigatti L, Narayanan RP, Diep T, McKeen D, Gang O, Stephanopoulos N, Sciortino F, Yan H, Romano F, Šulc P. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024; 384:776-781. [PMID: 38753798 DOI: 10.1126/science.adl5549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
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Affiliation(s)
- Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Thong Diep
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Flavio Romano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30171 Venezia-Mestre, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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2
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Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. J Chem Phys 2023; 158:074905. [PMID: 36813705 DOI: 10.1063/5.0134271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.
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Affiliation(s)
- Valerio Sorichetti
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, F-34095 Montpellier, France
| | | | | | | | | | - Cristian Micheletti
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Walter Kob
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, F-34095 Montpellier, France
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3
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Doye JPK, Fowler H, Prešern D, Bohlin J, Rovigatti L, Romano F, Šulc P, Wong CK, Louis AA, Schreck JS, Engel MC, Matthies M, Benson E, Poppleton E, Snodin BEK. The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami. Methods Mol Biol 2023; 2639:93-112. [PMID: 37166713 DOI: 10.1007/978-1-0716-3028-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
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Affiliation(s)
- Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Hannah Fowler
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Domen Prešern
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Joakim Bohlin
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
| | | | - Flavio Romano
- Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Chak Kui Wong
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, UK
| | - John S Schreck
- Computational and Information Systems Laboratory, National Center for Atmospheric Research (NCAR), Boulder, USA
| | - Megan C Engel
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Erik Benson
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK
| | - Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Benedict E K Snodin
- Department of Philosophy, Future of Humanity Institute, University of Oxford, Oxford, UK
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4
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Rovigatti L, Russo J, Romano F, Matthies M, Kroc L, Šulc P. A simple solution to the problem of self-assembling cubic diamond crystals. Nanoscale 2022; 14:14268-14275. [PMID: 36129342 DOI: 10.1039/d2nr03533b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The self-assembly of colloidal diamond (CD) crystals is considered as one of the most coveted goals of nanotechnology, both from the technological and fundamental points of view. For applications, colloidal diamond is a photonic crystal which can open new possibilities of manipulating light for information processing. From a fundamental point of view, its unique symmetry exacerbates a series of problems that are commonly faced during the self-assembly of target structures, such as the presence of kinetic traps and the formation of crystalline defects and alternative structures (polymorphs). Here we demonstrate that all these problems can be systematically addressed via SAT-assembly, a design framework that converts self-assembly into a Boolean satisfiability problem (SAT). Contrary to previous solutions (requiring four or more components), we prove that the assembly of the CD crystal only requires a binary mixture. Moreover, we use molecular dynamics simulations of a system composed by nearly a million nucleotides to test a DNA nanotechnology design that constitutes a promising candidate for experimental realization.
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Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy.
- CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy.
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
- European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
| | - Lukáš Kroc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
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5
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Rovigatti L, Sciortino F. Designing Enhanced Entropy Binding in Single-Chain Nanoparticles. Phys Rev Lett 2022; 129:047801. [PMID: 35939033 DOI: 10.1103/physrevlett.129.047801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/24/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Single-chain nanoparticles (SCNPs) are a new class of bio- and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or interpolymer bonds. Here we numerically show that a fully entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change-from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network-can be achieved by a judicious design of the patterns of reactive monomers along the polymer chain. Such a sensitivity arises from a delicate balance between the distinct entropic contributions controlling the binding.
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Affiliation(s)
- Lorenzo Rovigatti
- Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy and CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy
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6
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Russo J, Romano F, Kroc L, Sciortino F, Rovigatti L, Šulc P. SAT-assembly: a new approach for designing self-assembling systems. J Phys Condens Matter 2022; 34:354002. [PMID: 35148521 DOI: 10.1088/1361-648x/ac5479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure.
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Affiliation(s)
- John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
- European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Lukáš Kroc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, United States of America
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
- Institute for Complex Systems, Uos Sapienza, CNR, Rome 00185, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, United States of America
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7
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Biagi S, Rovigatti L, Abbasi M, Bureau L, Sciortino F, Misbah C. Hydrodynamic instability and flow reduction in polymer brush coated channels. Soft Matter 2021; 17:9235-9245. [PMID: 34596648 DOI: 10.1039/d1sm00638j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A polymer brush is a passive medium. At equilibrium the knowledge of its chemical composition and thickness is enough for a full system characterization. However, when the brush is exposed to fluid flow it reveals a much more intriguing nature, in which filamentous protrusions and the way they interact among themselves and with the surrounding fluid are of outmost importance. Here we investigate such a rich behavior via numerical simulations. We focus on the brush hydrodynamic response at low Reynolds numbers, observing a significant fluid flow reduction inside a polymer-brush coated channel. We find that the reduction of the flow inside the channel is significantly larger than what would happen if the brush effect consisted only in reducing the effective channel width. This amplified reduction is understood as being due to the morphological instability of the brush-liquid interface which is shown to have an elastic origin: the mechanical stress acting on the brush due to the imposed flow is partially released by the interface modulation. In turn, this modulation dissipates more energy than a flat interface in the surrounding fluid, causing a reduction of flow velocity. Our results and interpretations provide an explanation for recent experimental measurements.
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Affiliation(s)
- Sofia Biagi
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Mehdi Abbasi
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
| | - Lionel Bureau
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
- Istituto Sistemi Complessi (ISC), Via dei Taurini 19, 00185 Roma, Italy
| | - Chaouqi Misbah
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
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8
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Tauber J, Rovigatti L, Dussi S, van der Gucht J. Sharing the Load: Stress Redistribution Governs Fracture of Polymer Double Networks. Macromolecules 2021; 54:8563-8574. [PMID: 34602652 PMCID: PMC8482750 DOI: 10.1021/acs.macromol.1c01275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/28/2022]
Abstract
![]()
The stress response
of polymer double networks depends not only
on the properties of the constituent networks but also on the interactions
arising between them. Here, we demonstrate, via coarse-grained simulations,
that both their global stress response and their microscopic fracture
mechanics are governed by load sharing through these internetwork
interactions. By comparing our results with affine predictions, where
stress redistribution is by definition homogeneous, we show that stress
redistribution is highly inhomogeneous. In particular, the affine
prediction overestimates the fraction of broken chains by almost an
order of magnitude. Furthermore, homogeneous stress distribution predicts
a single fracture process, while in our simulations, fracture of sacrificial
chains takes place in two steps governed by load sharing within a
network and between networks, respectively. Our results thus provide
a detailed microscopic picture of how inhomogeneous stress redistribution
after rupture of chains governs the fracture of polymer double networks.
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Affiliation(s)
- Justin Tauber
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza-Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Simone Dussi
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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9
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Vialetto J, Camerin F, Grillo F, Ramakrishna SN, Rovigatti L, Zaccarelli E, Isa L. Effect of Internal Architecture on the Assembly of Soft Particles at Fluid Interfaces. ACS Nano 2021; 15:13105-13117. [PMID: 34328717 PMCID: PMC8388124 DOI: 10.1021/acsnano.1c02486] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Monolayers of soft colloidal particles confined at fluid interfaces are at the core of a broad range of technological processes, from the stabilization of responsive foams and emulsions to advanced lithographic techniques. However, establishing a fundamental relation between their internal architecture, which is controlled during synthesis, and their structural and mechanical properties upon interfacial confinement remains an elusive task. To address this open issue, which defines the monolayer's properties, we synthesize core-shell microgels, whose soft core can be chemically degraded in a controlled fashion. This strategy allows us to obtain a series of particles ranging from analogues of standard batch-synthesized microgels to completely hollow ones after total core removal. Combined experimental and numerical results show that our hollow particles have a thin and deformable shell, leading to a temperature-responsive collapse of the internal cavity and a complete flattening after adsorption at a fluid interface. Mechanical characterization shows that a critical degree of core removal is required to obtain soft disk-like particles at an oil-water interface, which present a distinct response to compression. At low packing fractions, the mechanical response of the monolayer is dominated by the outer polymer chains forming a corona surrounding the particles within the interfacial plane, regardless of the presence of a core. By contrast, at high compression, the absence of a core enables the particles to deform in the direction orthogonal to the interface and to be continuously compressed without altering the monolayer structure. These findings show how fine, single-particle architectural control during synthesis can be engineered to determine the interfacial behavior of microgels, enabling one to link particle conformation with the resulting material properties.
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Affiliation(s)
- Jacopo Vialetto
- Laboratory
for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Fabrizio Camerin
- CNR
Institute for Complex Systems, Uos Sapienza, P.le A. Moro 2, 00185 Roma, Italy
- Department
of Basic and Applied Sciences for Engineering, Sapienza University of Rome, via A. Scarpa 14, 00161 Roma, Italy
| | - Fabio Grillo
- Laboratory
for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Shivaprakash N. Ramakrishna
- Laboratory
for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Lorenzo Rovigatti
- CNR
Institute for Complex Systems, Uos Sapienza, P.le A. Moro 2, 00185 Roma, Italy
- Department
of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185 Roma, Italy
| | - Emanuela Zaccarelli
- CNR
Institute for Complex Systems, Uos Sapienza, P.le A. Moro 2, 00185 Roma, Italy
- Department
of Physics, Sapienza University of Rome, P.le A. Moro 2, 00185 Roma, Italy
| | - Lucio Isa
- Laboratory
for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
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10
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Affiliation(s)
- Maud Formanek
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR Cambridge, U.K
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
- CNR-ISC Uos Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
- CNR-ISC Uos Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
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11
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Poppleton E, Romero R, Mallya A, Rovigatti L, Šulc P. OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures. Nucleic Acids Res 2021; 49:W491-W498. [PMID: 34009383 PMCID: PMC8265093 DOI: 10.1093/nar/gkab324] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Roger Romero
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Lorenzo Rovigatti
- Department of Physics, Sapienza Università di Roma, P.le A. Moro 2 00185, Rome, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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12
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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13
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Sorichetti V, Ninarello A, Ruiz-Franco JM, Hugouvieux V, Kob W, Zaccarelli E, Rovigatti L. Effect of Chain Polydispersity on the Elasticity of Disordered Polymer Networks. Macromolecules 2021; 54:3769-3779. [PMID: 34054144 PMCID: PMC8154883 DOI: 10.1021/acs.macromol.1c00176] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/20/2021] [Indexed: 12/15/2022]
Abstract
Due to their unique structural and mechanical properties, randomly cross-linked polymer networks play an important role in many different fields, ranging from cellular biology to industrial processes. In order to elucidate how these properties are controlled by the physical details of the network (e.g., chain-length and end-to-end distributions), we generate disordered phantom networks with different cross-linker concentrations C and initial densities ρinit and evaluate their elastic properties. We find that the shear modulus computed at the same strand concentration for networks with the same C, which determines the number of chains and the chain-length distribution, depends strongly on the preparation protocol of the network, here controlled by ρinit. We rationalize this dependence by employing a generic stress-strain relation for polymer networks that does not rely on the specific form of the polymer end-to-end distance distribution. We find that the shear modulus of the networks is a nonmonotonic function of the density of elastically active strands, and that this behavior has a purely entropic origin. Our results show that if short chains are abundant, as it is always the case for randomly cross-linked polymer networks, the knowledge of the exact chain conformation distribution is essential for correctly predicting the elastic properties. Finally, we apply our theoretical approach to literature experimental data, qualitatively confirming our interpretations.
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Affiliation(s)
- Valerio Sorichetti
- Laboratoire
de Physique Théorique et Modéles Statistiques (LPTMS), CNRS, Université Paris-Saclay, F-91405 Orsay, France
- Laboratoire
Charles Coulomb (L2C), University of Montpellier,
CNRS, F-34095 Montpellier, France
- IATE,
University of Montpellier, INRAE, Institut Agro, F-34060 Montpellier, France
| | - Andrea Ninarello
- CNR-ISC
Uos Sapienza, Piazzale
A. Moro 2, IT-00185 Roma, Italy
- Department
of Physics, Sapienza Università di
Roma, Piazzale A. Moro
2, IT-00185 Roma, Italy
| | - José M. Ruiz-Franco
- CNR-ISC
Uos Sapienza, Piazzale
A. Moro 2, IT-00185 Roma, Italy
- Department
of Physics, Sapienza Università di
Roma, Piazzale A. Moro
2, IT-00185 Roma, Italy
| | - Virginie Hugouvieux
- IATE,
University of Montpellier, INRAE, Institut Agro, F-34060 Montpellier, France
| | - Walter Kob
- Laboratoire
Charles Coulomb (L2C), University of Montpellier,
CNRS, F-34095 Montpellier, France
- Institut
Universitaire de France, 75005 Paris, France
| | - Emanuela Zaccarelli
- CNR-ISC
Uos Sapienza, Piazzale
A. Moro 2, IT-00185 Roma, Italy
- Department
of Physics, Sapienza Università di
Roma, Piazzale A. Moro
2, IT-00185 Roma, Italy
| | - Lorenzo Rovigatti
- CNR-ISC
Uos Sapienza, Piazzale
A. Moro 2, IT-00185 Roma, Italy
- Department
of Physics, Sapienza Università di
Roma, Piazzale A. Moro
2, IT-00185 Roma, Italy
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14
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Del Monte G, Camerin F, Ninarello A, Gnan N, Rovigatti L, Zaccarelli E. Charge affinity and solvent effects in numerical simulations of ionic microgels. J Phys Condens Matter 2021; 33:084001. [PMID: 33105117 DOI: 10.1088/1361-648x/abc4cb] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ionic microgel particles are intriguing systems in which the properties of thermo-responsive polymeric colloids are enriched by the presence of charged groups. In order to rationalize their properties and predict the behaviour of microgel suspensions, it is necessary to develop a coarse-graining strategy that starts from the accurate modelling of single particles. Here, we provide a numerical advancement of a recently-introduced model for charged co-polymerized microgels by improving the treatment of ionic groups in the polymer network. We investigate the thermoresponsive properties of the particles, in particular their swelling behaviour and structure, finding that, when charged groups are considered to be hydrophilic at all temperatures, highly charged microgels do not achieve a fully collapsed state, in favorable comparison to experiments. In addition, we explicitly include the solvent in the description and put forward a mapping between the solvophobic potential in the absence of the solvent and the monomer-solvent interactions in its presence, which is found to work very accurately for any charge fraction of the microgel. Our work paves the way for comparing single-particle properties and swelling behaviour of ionic microgels to experiments and to tackle the study of these charged soft particles at a liquid-liquid interface.
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Affiliation(s)
- Giovanni Del Monte
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
- Center for Life NanoScience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Fabrizio Camerin
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, via Antonio Scarpa 14, 00161 Roma, Italy
| | - Andrea Ninarello
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Nicoletta Gnan
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Lorenzo Rovigatti
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
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15
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Ventura Rosales IE, Rovigatti L, Bianchi E, Likos CN, Locatelli E. Shape control of soft patchy nanoparticles under confinement. Nanoscale 2020; 12:21188-21197. [PMID: 33034608 DOI: 10.1039/d0nr05058j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular building blocks undergoing a hierarchical assembly process form nano-scale objects which can further assemble into supramolecular structures. When the intermediate units have a limited valence in bonding, complex structures with tailored properties can be created. Here, we consider a composite, star-shaped particle made of f diblock copolymer chains uniformly grafted on a spherical colloid and investigate its first self-assembly stage both in the bulk and under lateral confinement. By means of numerical simulations, we show that, in the bulk, this system develops aggregates whose number and size depend on the temperature as well as on the relative ratio of solvophobic monomers. The emerging aggregates are referred to as patches and impart directionality in bonding to the complex particle. We further characterize how we can control, by changing the lateral confinement, the shape of the brush and the patch properties as a function of the distance between the confining walls. We find that the number of the patches can be determined by tuning the degree of confinement imposed on the particle. Finally, we employ a continuum mechanics model, known as the Liquid Drop Model, to gain insight into the elastic properties of the system. This theoretical approach allows to connect the patch properties to the elastic response of the composite particle.
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16
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Heidenreich M, Georgeson JM, Locatelli E, Rovigatti L, Nandi SK, Steinberg A, Nadav Y, Shimoni E, Safran SA, Doye JPK, Levy ED. Designer protein assemblies with tunable phase diagrams in living cells. Nat Chem Biol 2020; 16:939-945. [PMID: 32661377 DOI: 10.1038/s41589-020-0576-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Protein self-organization is a hallmark of biological systems. Although the physicochemical principles governing protein-protein interactions have long been known, the principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remain challenging to characterize. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies. We devise a new strategy to map high-resolution phase diagrams in living cells, which provide self-assembly signatures of this system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how interaction affinity impacts the phase diagram and material state of the assemblies in vivo. The phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Finally, we find that cotranslational protein binding suffices to recruit a messenger RNA to the designed micron-scale structures.
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Affiliation(s)
- Meta Heidenreich
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph M Georgeson
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lorenzo Rovigatti
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Physics, Sapienza Università di Roma, Rome, Italy.
| | - Saroj Kumar Nandi
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Avital Steinberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Nadav
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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17
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Del Monte G, Ninarello A, Camerin F, Rovigatti L, Gnan N, Zaccarelli E. Numerical insights on ionic microgels: structure and swelling behaviour. Soft Matter 2019; 15:8113-8128. [PMID: 31589214 DOI: 10.1039/c9sm01253b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent progress has been made in the numerical modelling of neutral microgel particles with a realistic, disordered structure. In this work we extend this approach to the case of co-polymerised microgels where a thermoresponsive polymer is mixed with acidic groups. We compare the cases where counterions directly interact with microgel charges or are modelled implicitly through a Debye-Hückel description. We do so by performing extensive numerical simulations of single microgels across the volume phase transition (VPT) varying the temperature and the fraction of charged monomers. We find that the presence of charges considerably alters the microgel structure, quantified by the monomer density profiles and by the form factors of the microgels, particularly close to the VPT. We observe significant deviations between the implicit and explicit models, with the latter comparing more favourably to available experiments. In particular, we observe a shift of the VPT temperature to larger values as the amount of charged monomers increases. We also find that below the VPT the microgel-counterion complex is almost neutral, while it develops a net charge above the VPT. Interestingly, under these conditions the collapsed microgel still retains a large amount of counterions inside its structure. Since these interesting features cannot be captured by the implicit model, our results show that it is crucial to explicitly include the counterions in order to realistically model ionic thermoresponsive microgels.
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Affiliation(s)
- Giovanni Del Monte
- Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and Center for Life NanoScience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Andrea Ninarello
- CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy.
| | - Fabrizio Camerin
- CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, via A. Scarpa 14, 00161 Rome, Italy
| | - Lorenzo Rovigatti
- Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy.
| | - Nicoletta Gnan
- CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy.
| | - Emanuela Zaccarelli
- CNR-ISC, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy. and Physics Department, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy.
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18
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Ninarello A, Crassous JJ, Paloli D, Camerin F, Gnan N, Rovigatti L, Schurtenberger P, Zaccarelli E. Modeling Microgels with a Controlled Structure across the Volume Phase Transition. Macromolecules 2019; 52:7584-7592. [PMID: 31656322 PMCID: PMC6812067 DOI: 10.1021/acs.macromol.9b01122] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/20/2019] [Indexed: 12/13/2022]
Abstract
![]()
Thermoresponsive microgels are soft
colloids that find widespread
use as model systems for soft matter physics. Their complex internal
architecture, made of a disordered and heterogeneous polymer network,
has been so far a major challenge for computer simulations. In this
work, we put forward a coarse-grained model of microgels whose structural
properties are in quantitative agreement with results obtained with
small-angle X-ray scattering experiments across a wide range of temperatures,
encompassing the volume phase transition. These results bridge the
gap between experiments and simulations of individual microgel particles,
paving the way to theoretically address open questions about their
bulk properties with unprecedented nano- and microscale resolution.
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Affiliation(s)
- Andrea Ninarello
- CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy.,Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy
| | - Jérôme J Crassous
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, DE-52074 Aachen, Germany.,Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 14, SE-22100 Lund, Sweden
| | - Divya Paloli
- Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 14, SE-22100 Lund, Sweden
| | - Fabrizio Camerin
- CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy.,Department of Basic and Applied Sciences for Engineering, Sapienza Università di Roma, via A. Scarpa 14, IT-00161 Roma, Italy
| | - Nicoletta Gnan
- CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy.,Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy
| | - Lorenzo Rovigatti
- Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy.,CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy
| | - Peter Schurtenberger
- Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 14, SE-22100 Lund, Sweden
| | - Emanuela Zaccarelli
- CNR-ISC Uos Sapienza, Piazzale A. Moro 2, IT-00185 Roma, Italy.,Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, IT-00185 Roma, Italy
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19
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Suma A, Poppleton E, Matthies M, Šulc P, Romano F, Louis AA, Doye JPK, Micheletti C, Rovigatti L. TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. J Comput Chem 2019; 40:2586-2595. [PMID: 31301183 DOI: 10.1002/jcc.26029] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/11/2022]
Abstract
Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122.,SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062, Dresden, Germany
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, Via Torino, 155, 30172, Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Cristian Micheletti
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Universitá di Roma, Piazzale A. Moro, 2, 00185, Rome, Italy.,CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Rome, Italy
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20
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Rovigatti L, Gnan N, Ninarello A, Zaccarelli E. Connecting Elasticity and Effective Interactions of Neutral Microgels: The Validity of the Hertzian Model. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00099] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Nicoletta Gnan
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Andrea Ninarello
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
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21
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Abstract
Investigating million-atom systems for very long simulation times, we demonstrate that the collective density-density correlation time (τ_{α}) in simulated supercooled water and silica becomes wave-vector independent (q^{0}) when the probing wavelength is several times larger than the interparticle distance. The q independence of the collective density-density correlation functions, a feature clearly observed in light-scattering studies of some soft-matter systems, is thus a genuine feature of many (but not all) slow-dynamics systems, either atomic, molecular, or colloidal. Indeed, we show that when the dynamics of the density fluctuations includes particle-type diffusion, as in the case of the Lennard-Jones binary-mixture model, the q^{0} regime does not set in and the relaxation time continues to scale as τ_{α}∼q^{-2} even at small q.
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Affiliation(s)
- Philip H Handle
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Lorenzo Rovigatti
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- CNR-ISC, UoS Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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22
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Camerin F, Fernández-Rodríguez MÁ, Rovigatti L, Antonopoulou MN, Gnan N, Ninarello A, Isa L, Zaccarelli E. Microgels Adsorbed at Liquid-Liquid Interfaces: A Joint Numerical and Experimental Study. ACS Nano 2019; 13:4548-4559. [PMID: 30865829 DOI: 10.1021/acsnano.9b00390] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Soft particles display highly versatile properties with respect to hard colloids and even more so at fluid-fluid interfaces. In particular, microgels, consisting of a cross-linked polymer network, are able to deform and flatten upon adsorption at the interface due to the balance between surface tension and internal elasticity. Despite the existence of experimental results, a detailed theoretical understanding of this phenomenon is still lacking due to the absence of appropriate microscopic models. In this work, we propose an advanced modeling of microgels at a flat water/oil interface. The model builds on a realistic description of the internal polymeric architecture and single-particle properties of the microgel and is able to reproduce its experimentally observed shape at the interface. Complementing molecular dynamics simulations with in situ cryo-electron microscopy experiments and atomic force microscopy imaging after Langmuir-Blodgett deposition, we compare the morphology of the microgels for different values of the cross-linking ratios. Our model allows for a systematic microscopic investigation of soft particles at fluid interfaces, which is essential to develop predictive power for the use of microgels in a broad range of applications, including the stabilization of smart emulsions and the versatile patterning of surfaces.
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Affiliation(s)
- Fabrizio Camerin
- CNR Institute for Complex Systems, Uos Sapienza , Piazzale Aldo Moro 2 , 00185 Roma , Italy
- Department of Basic and Applied Sciences for Engineering , Sapienza University of Rome , Via Antonio Scarpa 14 , 00161 Roma , Italy
| | - Miguel Ángel Fernández-Rodríguez
- Laboratory for Interfaces, Soft Matter and Assembly, Department of Materials , ETH Zürich , Vladimir-Prelog-Weg 5 , 8093 Zürich , Switzerland
| | - Lorenzo Rovigatti
- CNR Institute for Complex Systems, Uos Sapienza , Piazzale Aldo Moro 2 , 00185 Roma , Italy
- Department of Physics , Sapienza University of Rome , Piazzale Aldo Moro 2 , 00185 Roma , Italy
| | - Maria-Nefeli Antonopoulou
- Laboratory for Interfaces, Soft Matter and Assembly, Department of Materials , ETH Zürich , Vladimir-Prelog-Weg 5 , 8093 Zürich , Switzerland
| | - Nicoletta Gnan
- CNR Institute for Complex Systems, Uos Sapienza , Piazzale Aldo Moro 2 , 00185 Roma , Italy
- Department of Physics , Sapienza University of Rome , Piazzale Aldo Moro 2 , 00185 Roma , Italy
| | - Andrea Ninarello
- CNR Institute for Complex Systems, Uos Sapienza , Piazzale Aldo Moro 2 , 00185 Roma , Italy
- Department of Physics , Sapienza University of Rome , Piazzale Aldo Moro 2 , 00185 Roma , Italy
| | - Lucio Isa
- Laboratory for Interfaces, Soft Matter and Assembly, Department of Materials , ETH Zürich , Vladimir-Prelog-Weg 5 , 8093 Zürich , Switzerland
| | - Emanuela Zaccarelli
- CNR Institute for Complex Systems, Uos Sapienza , Piazzale Aldo Moro 2 , 00185 Roma , Italy
- Department of Physics , Sapienza University of Rome , Piazzale Aldo Moro 2 , 00185 Roma , Italy
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23
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Rovigatti L, Gnan N, Tavagnacco L, Moreno AJ, Zaccarelli E. Numerical modelling of non-ionic microgels: an overview. Soft Matter 2019; 15:1108-1119. [PMID: 30543246 PMCID: PMC6371763 DOI: 10.1039/c8sm02089b] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 11/26/2018] [Indexed: 05/03/2023]
Abstract
Microgels are complex macromolecules. These colloid-sized polymer networks possess internal degrees of freedom and, depending on the polymer(s) they are made of, can acquire a responsiveness to variations of the environment (temperature, pH, salt concentration, etc.). Besides being valuable for many practical applications, microgels are also extremely important to tackle fundamental physics problems. As a result, these last years have seen a rapid development of protocols for the synthesis of microgels, and more and more research has been devoted to the investigation of their bulk properties. However, from a numerical standpoint the picture is more fragmented, as the inherently multi-scale nature of microgels, whose bulk behaviour crucially depends on the microscopic details, cannot be handled at a single level of coarse-graining. Here we present an overview of the methods and models that have been proposed to describe non-ionic microgels at different length-scales, from the atomistic to the single-particle level. We especially focus on monomer-resolved models, as these have the right level of details to capture the most important properties of microgels, responsiveness and softness. We suggest that these microscopic descriptions, if realistic enough, can be employed as starting points to develop the more coarse-grained representations required to investigate the behaviour of bulk suspensions.
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Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica
, Sapienza Università di Roma
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
- CNR-ISC
, Uos Sapienza
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
| | - Nicoletta Gnan
- Dipartimento di Fisica
, Sapienza Università di Roma
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
- CNR-ISC
, Uos Sapienza
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
| | - Letizia Tavagnacco
- Dipartimento di Fisica
, Sapienza Università di Roma
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
- CNR-ISC
, Uos Sapienza
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC
,
Paseo Manuel de Lardizabal 5
, 20018 San Sebastián
, Spain
- Donostia International Physics Center
,
Paseo Manuel de Lardizabal 4
, 20018 San Sebastian
, Spain
| | - Emanuela Zaccarelli
- Dipartimento di Fisica
, Sapienza Università di Roma
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
- CNR-ISC
, Uos Sapienza
,
Piazzale A. Moro 2
, 00185 Roma
, Italy
.
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24
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Cardelli C, Bianco V, Rovigatti L, Nerattini F, Tubiana L, Dellago C, Coluzza I. Author Correction: The role of directional interactions in the designability of generalized heteropolymers. Sci Rep 2018. [PMID: 29531260 PMCID: PMC5847616 DOI: 10.1038/s41598-018-22649-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Bergman MJ, Gnan N, Obiols-Rabasa M, Meijer JM, Rovigatti L, Zaccarelli E, Schurtenberger P. A new look at effective interactions between microgel particles. Nat Commun 2018; 9:5039. [PMID: 30487527 PMCID: PMC6262015 DOI: 10.1038/s41467-018-07332-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022] Open
Abstract
Thermoresponsive microgels find widespread use as colloidal model systems, because their temperature-dependent size allows facile tuning of their volume fraction in situ. However, an interaction potential unifying their behavior across the entire phase diagram is sorely lacking. Here we investigate microgel suspensions in the fluid regime at different volume fractions and temperatures, and in the presence of another population of small microgels, combining confocal microscopy experiments and numerical simulations. We find that effective interactions between microgels are clearly temperature dependent. In addition, microgel mixtures possess an enhanced stability compared to hard colloid mixtures - a property not predicted by a simple Hertzian model. Based on numerical calculations we propose a multi-Hertzian model, which reproduces the experimental behavior for all studied conditions. Our findings highlight that effective interactions between microgels are much more complex than usually assumed, displaying a crucial dependence on temperature and on the internal core-corona architecture of the particles.
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Affiliation(s)
- Maxime J Bergman
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Nicoletta Gnan
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185, Roma, Italy
| | - Marc Obiols-Rabasa
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden.,CR Competence AB, Naturvetarevägen 14, 22362, Lund, Sweden
| | - Janne-Mieke Meijer
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden.,Department of Physics, University of Konstanz, PO Box 688, D-78457, Konstanz, Germany
| | - Lorenzo Rovigatti
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185, Roma, Italy
| | - Emanuela Zaccarelli
- CNR-ISC and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185, Roma, Italy.
| | - Peter Schurtenberger
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden.
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26
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Abstract
Thermoresponsive microgels are polymeric colloidal networks that can change their size in response to a temperature variation. This peculiar feature is driven by the nature of the solvent-polymer interactions, which triggers the so-called volume phase transition from a swollen to a collapsed state above a characteristic temperature. Recently, an advanced modelling protocol to assemble realistic, disordered microgels has been shown to reproduce experimental swelling behavior and form factors. In the original framework, the solvent was taken into account in an implicit way, condensing solvent-polymer interactions in an effective attraction between monomers. To go one step further, in this work we perform simulations of realistic microgels in an explicit solvent. We identify a suitable model which fully captures the main features of the implicit model and further provides information on the solvent uptake by the interior of the microgel network and on its role in the collapse kinetics. These results pave the way for addressing problems where solvent effects are dominant, such as the case of microgels at liquid-liquid interfaces.
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Affiliation(s)
- F Camerin
- CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Roma, Italy.
- Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Sapienza Università di Roma, via A. Scarpa, 14, 00161, Roma, Italy.
| | - N Gnan
- CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro, 2, 00185, Roma, Italy
| | - L Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro, 2, 00185, Roma, Italy
| | - E Zaccarelli
- CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Roma, Italy.
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro, 2, 00185, Roma, Italy.
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27
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Rovigatti L, Romano F, Russo J. Topical Issue on Advances in Computational Methods for Soft Matter Systems. Eur Phys J E Soft Matter 2018; 41:98. [PMID: 30143882 DOI: 10.1140/epje/i2018-11695-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185, Roma, Italy
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, 30172, Venezia Mestre, Italy
| | - John Russo
- School of Mathematics, University of Bristol, BS8 1TW, Bristol, UK
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28
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Engel MC, Smith DM, Jobst MA, Sajfutdinow M, Liedl T, Romano F, Rovigatti L, Louis AA, Doye JPK. Force-Induced Unravelling of DNA Origami. ACS Nano 2018; 12:6734-6747. [PMID: 29851456 DOI: 10.1021/acsnano.8b01844] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.
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Affiliation(s)
- Megan C Engel
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Markus A Jobst
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Martin Sajfutdinow
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Tim Liedl
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Università Ca' Foscari di Venezia , Via Torino 155 , 30172 Venezia Mestre , Italy
| | - Lorenzo Rovigatti
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
- CNR-ISC , Uos Sapienza, Piazzale A. Moro 2 , 00185 Roma , Italy
- Dipartimento di Fisica , Sapienza Università di Roma , Piazzale A. Moro 2 , 00185 Roma , Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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29
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Ruiz-Franco J, Rovigatti L, Zaccarelli E. On the effect of the thermostat in non-equilibrium molecular dynamics simulations. Eur Phys J E Soft Matter 2018; 41:80. [PMID: 29955976 DOI: 10.1140/epje/i2018-11689-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters.
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Affiliation(s)
- José Ruiz-Franco
- Dipartimento di Fisica, Sapienza Università di Roma, P.le A. Moro 5, 00185, Roma, Italy.
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le A. Moro 5, 00185, Roma, Italy
- CNR Institute for Complex Systems (ISC), Uos Sapienza, Roma, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Sapienza Università di Roma, P.le A. Moro 5, 00185, Roma, Italy
- CNR Institute for Complex Systems (ISC), Uos Sapienza, Roma, Italy
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30
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Abstract
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free-energy methods. The review is complemented by an educationally oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model.
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Affiliation(s)
- Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185, Roma, Italy.
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185, Roma, Italy.
| | - John Russo
- School of Mathematics, University of Bristol, BS8 1TW, Bristol, UK
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, 30172, Venezia Mestre, Italy
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31
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Locatelli E, Rovigatti L. An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids. Polymers (Basel) 2018; 10:E447. [PMID: 30966482 PMCID: PMC6415226 DOI: 10.3390/polym10040447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 12/30/2022] Open
Abstract
We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.
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Affiliation(s)
- Emanuele Locatelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
| | - Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy.
- Department of Physics, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy.
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32
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Cardelli C, Bianco V, Rovigatti L, Nerattini F, Tubiana L, Dellago C, Coluzza I. Are Proteins Such Unique Polymers? - The Role of Directional Interactions in the Designability of Generalized Heteropolymers. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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33
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Abstract
Microgels are soft colloids that, by virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as well as for many diverse practical applications, ranging from art restoration to medicine. Such an extraordinary versatility stems from the complex internal structure of the individual microgels, each of which is a crosslinked polymer network. Here we employ a recently-introduced computational method to generate realistic microgel configurations and look at their structural properties, both in real and Fourier space, for several temperatures across the volume phase transition as a function of the crosslinker concentration and of the confining radius employed during the 'in-silico' synthesis. We find that the chain-length distribution of the resulting networks can be analytically predicted by a simple theoretical argument. In addition, we find that our results are well-fitted to the fuzzy-sphere model, which correctly reproduces the density profile of the microgels under study.
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Affiliation(s)
- Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy. Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
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34
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Affiliation(s)
- Lorenzo Rovigatti
- CNR-ISC,
Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
- Department
of Physics, Sapienza, Universitá di Roma, Piazzale Aldo
Moro 2, I-00185, Roma, Italy
| | - Giovanni Nava
- Department
of Medical Biotechnology and Translational Medicine, Universita degli Studi di Milano, via Fratelli Cervi 93, I-20090 Segrate, MI, Italy
| | - Tommaso Bellini
- Department
of Medical Biotechnology and Translational Medicine, Universita degli Studi di Milano, via Fratelli Cervi 93, I-20090 Segrate, MI, Italy
| | - Francesco Sciortino
- Department
of Physics, Sapienza, Universitá di Roma, Piazzale Aldo
Moro 2, I-00185, Roma, Italy
| |
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35
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Abstract
Microgels are colloidal-scale particles individually made of cross-linked polymer networks that can swell and deswell in response to external stimuli, such as changes to temperature or pH. Despite a large amount of experimental activities on microgels, a proper theoretical description based on individual particle properties is still missing due to the complexity of the particles. To go one step further, here we propose a novel methodology to assemble realistic microgel particles in silico. We exploit the self-assembly of a binary mixture composed of tetravalent (cross-linkers) and bivalent (monomer beads) patchy particles under spherical confinement in order to produce fully bonded networks. The resulting structure is then used to generate the initial microgel configuration, which is subsequently simulated with a bead-spring model complemented by a temperature-induced hydrophobic attraction. To validate our assembly protocol, we focus on a small microgel test case and show that we can reproduce the experimental swelling curve by appropriately tuning the confining sphere radius, something that would not be possible with less sophisticated assembly methodologies, e.g., in the case of networks generated from an underlying crystal structure. We further investigate the structure (in reciprocal and real space) and the swelling curves of microgels as a function of temperature, finding that our results are well described by the widely used fuzzy sphere model. This is a first step toward a realistic modeling of microgel particles, which will pave the way for a careful assessment of their elastic properties and effective interactions.
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Affiliation(s)
- Nicoletta Gnan
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale A. Moro
2, 00185 Roma, Italy
| | - Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale A. Moro
2, 00185 Roma, Italy
| | - Maxime Bergman
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund, Sweden
| | - Emanuela Zaccarelli
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale A. Moro
2, 00185 Roma, Italy
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36
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Ronti M, Rovigatti L, Tavares JM, Ivanov AO, Kantorovich SS, Sciortino F. Free energy calculations for rings and chains formed by dipolar hard spheres. Soft Matter 2017; 13:7870-7878. [PMID: 29019510 DOI: 10.1039/c7sm01692a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We employ a method based on Monte Carlo grand-canonical simulations to precisely calculate partition functions of non-interacting chains and rings formed by dipolar hard spheres (DHS) at low temperature. The extended low temperature region offered by such cluster calculations, compared to what had been previously achieved with standard simulations, opens up the possibility of exploring a part of the DHS phase diagram which was inaccessible before. The reported results offer the unique opportunity of verifying well-established theoretical models based on the ideal gas of cluster approximation in order to clarify their range of validity. They also provide the basis for future studies in which cluster-cluster interactions will be included.
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Affiliation(s)
- Michela Ronti
- University of Vienna, Sensengasse 8, 1090 Vienna, Austria.
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37
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C. Gârlea I, Bianchi E, Capone B, Rovigatti L, N. Likos C. Hierarchical self-organization of soft patchy nanoparticles into morphologically diverse aggregates. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Abstract
We present a numerical/theoretical approach to efficiently evaluate the phase diagram of self-assembling DNA nanostars. Combining input information based on a realistic coarse-grained DNA potential with the Wertheim association theory, we derive a parameter-free thermodynamic description of these systems. We apply this method to investigate the phase behavior of single components and mixtures of DNA nanostars with different numbers of sticky arms, elucidating the role of the system functionality and of salt concentration. Specifically, we evaluate the propensity to demix, the gas-liquid phase boundaries and the location of the critical points. The predicted critical parameters compare very well with existing experimental results for the available compositions. The approach developed here is very general, easily extensible to other all-DNA systems, and provides guidance for future experiments.
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Affiliation(s)
- Emanuele Locatelli
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- E-mail:
| | - Philip H. Handle
- Dipartimento
di Fisica, Sapienza-Università di
Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Francesco Sciortino
- Dipartimento
di Fisica, Sapienza-Università di
Roma, Piazzale A. Moro 5, 00185 Roma, Italy
- Istituto
Sistemi Complessi (CNR-ISC), Via dei Taurini 19, 00185 Roma, Italy
| | - Lorenzo Rovigatti
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Rudolf
Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, U.K.
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39
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Fernandez-Castanon J, Bomboi F, Rovigatti L, Zanatta M, Paciaroni A, Comez L, Porcar L, Jafta CJ, Fadda GC, Bellini T, Sciortino F. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars. J Chem Phys 2017; 145:084910. [PMID: 27586949 DOI: 10.1063/1.4961398] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.
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Affiliation(s)
| | - F Bomboi
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - L Rovigatti
- Rudolf Peierls C.T.P., University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - M Zanatta
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - A Paciaroni
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Comez
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - C J Jafta
- Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - G C Fadda
- Laboratoire Léon Brillouin, LLB, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - T Bellini
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, I-20133 Milano, Italy
| | - F Sciortino
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
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40
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Rovigatti L, Bianco V, Tavares JM, Sciortino F. Communication: Re-entrant limits of stability of the liquid phase and the Speedy scenario in colloidal model systems. J Chem Phys 2017; 146:041103. [DOI: 10.1063/1.4974830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lorenzo Rovigatti
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - José Maria Tavares
- Instituto Superior de Engenharia de Lisboa-ISEL, Rua Conselheiro Emídio Navarro 1, P-1950-062 Lisbon, Portugal and Centro de Física Teórica e Computacional, Universidade de Lisboa, Campo Grande, P-1749-016 Lisbon, Portugal
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy and Istituto Sistemi Complessi (CNR-ISC), Via dei Taurini 19, 00185 Roma, Italy
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41
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Abstract
We report a detailed computational study by Brownian dynamics simulations of the structure and dynamics of a liquid of patchy particles which forms an amorphous tetrahedral network upon decreasing the temperature. The highly directional particle interactions allow us to investigate the system connectivity by discriminating the total set of particles into different populations according to a penta-modal distribution of bonds per particle. With this methodology we show how the particle bonding process is not randomly independent but it manifests clear bond correlations at low temperatures. We further explore the dynamics of the system in real space and establish a clear relation between particle mobility and particle connectivity. In particular, we provide evidence of anomalous diffusion at low temperatures and reveal how the dynamics is affected by the short-time hopping motion of the weakly bounded particles. Finally we widely investigate the dynamics and structure of the system in Fourier space and identify two quantitatively similar length scales, one dynamic and the other static, which increase upon cooling the system and reach distances of the order of few particle diameters. We summarize our findings in a qualitative picture where the low temperature regime of the viscoelastic liquid is understood in terms of an evolving network of long time metastable cooperative domains of particles.
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Affiliation(s)
- Sándalo Roldán-Vargas
- Max Planck Institute for the Physics of Complex Systems, D-01307, Dresden, Germany. and Department of Physics, Sapienza, Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Lorenzo Rovigatti
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP, UK
| | - Francesco Sciortino
- Department of Physics, Sapienza, Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
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42
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Bianchi E, Capone B, Coluzza I, Rovigatti L, van Oostrum PDJ. Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules. Phys Chem Chem Phys 2017; 19:19847-19868. [DOI: 10.1039/c7cp03149a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).
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Affiliation(s)
- Emanuela Bianchi
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Institute for Theoretical Physics
| | - Barbara Capone
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Dipartimento di Scienze
| | - Ivan Coluzza
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - Lorenzo Rovigatti
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Rudolf Peierls Centre for Theoretical Physics
| | - Peter D. J. van Oostrum
- Department of Nanobiotechnology
- Institute for Biologically Inspired Materials
- University of Natural Resources and Life Sciences
- A-1190 Vienna
- Austria
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43
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Mahynski NA, Rovigatti L, Likos CN, Panagiotopoulos AZ. Void-Based Assembly of Colloidal Crystals: Using Structure-Directing Agents to Direct the Assembly of Open Colloidal Crystals. GIT Lab J Eur 2016; 5:1-5. [PMID: 31080380 PMCID: PMC6506831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have used computer simulations to reveal how colloidal crystals may be assembled by engineering the shape and charge of polymeric additives, which act as structure-directing agents (SDAs). Using these agents, only a single desired polymorph may be obtained from a crystallizing mixture of colloids and polymers, which would otherwise result in a defective crystal in the absence of these agents. Building on previous work, which demonstrated this principle in the limiting case of high-density, close-packed crystals, we have now achieved this control over low-density, open crystals, which have broad utility especially in optical applications. These results reveal the general utility of the SDA paradigm in assembling tailored colloidal crystals, which represents a new design method that does not rely on any modification of the colloids themselves.
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Affiliation(s)
- Nathan A. Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Lorenzo Rovigatti
- Rudolph Peierls Centre for Theoretical Physics, Oxford University, Oxford, UK
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44
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Mahynski NA, Rovigatti L, Likos C, Panagiotopoulos A. Bottom-Up Colloidal Crystal Assembly with a Twist. ACS Nano 2016; 10:5459-67. [PMID: 27124487 PMCID: PMC4881195 DOI: 10.1021/acsnano.6b01854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/28/2016] [Indexed: 05/28/2023]
Abstract
Globally ordered colloidal crystal lattices have broad utility in a wide range of optical and catalytic devices, for example, as photonic band gap materials. However, the self-assembly of stereospecific structures is often confounded by polymorphism. Small free-energy differences often characterize ensembles of different structures, making it difficult to produce a single morphology at will. Current techniques to handle this problem adopt one of two approaches: that of the "top-down" or "bottom-up" methodology, whereby structures are engineered starting from the largest or smallest relevant length scales, respectively. However, recently, a third approach for directing high fidelity assembly of colloidal crystals has been suggested which relies on the introduction of polymer cosolutes into the crystal phase [Mahynski, N.; Panagiotopoulos, A. Z.; Meng, D.; Kumar, S. K. Nat. Commun. 2014, 5, 4472]. By tuning the polymer's morphology to interact uniquely with the void symmetry of a single desired crystal, the entropy loss associated with polymer confinement has been shown to strongly bias the formation of that phase. However, previously, this approach has only been demonstrated in the limiting case of close-packed crystals. Here, we show how this approach may be generalized and extended to complex open crystals, illustrating the utility of this "structure-directing agent" paradigm in engineering the nanoscale structure of ordered colloidal materials. The high degree of transferability of this paradigm's basic principles between relatively simple crystals and more complex ones suggests that this represents a valuable addition to presently known self-assembly techniques.
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Affiliation(s)
- Nathan A. Mahynski
- Chemical
Informatics Research Group, Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, United States
| | - Lorenzo Rovigatti
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Christos
N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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45
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Abstract
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
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Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lorenzo Rovigatti
- Faculty of Physics, University of Vienna , Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford, OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
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46
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Abstract
The fabrication of versatile building blocks that reliably self-assemble into desired ordered and disordered phases is amongst the hottest topics in contemporary materials science. To this end, microscopic units of varying complexity, aimed at assembling the target phases, have been thought, designed, investigated and built. Such a path usually requires laborious fabrication techniques, especially when specific functionalisation of the building blocks is required. Telechelic star polymers, i.e., star polymers made of a number of f di-block copolymers consisting of solvophobic and solvophilic monomers grafted on a central anchoring point, spontaneously self-assemble into soft patchy particles featuring attractive spots (patches) on the surface. Here we show that the tunability of such a system can be widely extended by controlling the physical and chemical parameters of the solution. Indeed, under fixed external conditions the self-assembly behaviour depends only on the number of arms and on the ratio of solvophobic to solvophilic monomers. However, changes in temperature and/or solvent quality make it possible to reliably change the number and size of the attractive patches. This allows the steering of the mesoscopic self-assembly behaviour without modifying the microscopic constituents. Interestingly, we also demonstrate that diverse combinations of the parameters can generate stars with the same number of patches but different radial and angular stiffness. This mechanism could provide a neat way of further fine-tuning the elastic properties of the supramolecular network without changing its topology.
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Affiliation(s)
- Lorenzo Rovigatti
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
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47
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Abstract
We investigate binary mixtures of large colloids interacting through soft potentials with small, ideal depletants. We show that softness has a dramatic effect on the resulting colloid-colloid effective potential when the depletant-to-colloid size ratio q is small, with significant consequences on the colloidal phase behaviour. We provide an exact relationship that allows us to obtain the effective pair potential for any type of colloid-depletant interaction in the case of ideal depletants, without having to rely on complicated and expensive full-mixture simulations. We also show that soft repulsion among depletants further enhances the tendency of colloids to aggregate. Our theoretical and numerical results demonstrate that--in the limit of small q--soft mixtures cannot be mapped onto hard systems and hence soft depletion is not a mere extension of the widely used Asakura-Oosawa potential.
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Affiliation(s)
- Lorenzo Rovigatti
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
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48
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Kantorovich SS, Ivanov AO, Rovigatti L, Tavares JM, Sciortino F. Temperature-induced structural transitions in self-assembling magnetic nanocolloids. Phys Chem Chem Phys 2015; 17:16601-8. [DOI: 10.1039/c5cp01558h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
With the help of a unique combination of density functional theory and computer simulations, we discover two possible scenarios, depending on concentration, for the hierarchical self-assembly of magnetic nanoparticles on cooling.
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Affiliation(s)
| | | | | | - Jose M. Tavares
- Centro de Física Teórica e Computacional da Universidade de Lisboa
- Faculdade de Ciências
- Campo Grande
- 1749-016 Lisboa
- Portugal
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49
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Rovigatti L, Šulc P, Reguly IZ, Romano F. A comparison between parallelization approaches in molecular dynamics simulations on GPUs. J Comput Chem 2014; 36:1-8. [DOI: 10.1002/jcc.23763] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica; Sapienza-Università di Roma; Piazzale A. Moro 5 00185 Roma Italy
- Faculty of Physics; University of Vienna; Boltzmanngasse 5 A-1090 Vienna Austria
| | - Petr Šulc
- Department of Physics, Rudolf Peierls Centre for Theoretical Physics; University of Oxford; 1 Keble Road Oxford OX1 3NP United Kingdom
| | - István Z. Reguly
- Mathematical, Physical and Life Sciences Division; Oxford e-Research Centre, University of Oxford; Oxford, 7 Keble Road Oxford OX1 3QG United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry; University of Oxford; South Parks Road Oxford OX1 3QZ United Kingdom
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50
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Abstract
Using state-of-the-art numerical techniques, we show that, upon lowering the temperature, tetravalent DNA nanostars form a thermodynamically stable, fully bonded equilibrium gel. In contrast to atomic and molecular network formers, in which the disordered liquid is always metastable with respect to some crystalline phase, we find that the DNA nanostar gel has a lower free energy than the diamond crystal structure in a wide range of concentrations. This unconventional behavior, here verified for the first time in a realistic model, arises from the large arm flexibility of the DNA nanostars, a property that can be tuned by design. Our results confirm the thermodynamic stability of the recently experimentally realized DNA hydrogels.
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Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma , Piazzale A. Moro 2, 00185 Roma, Italy
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