1
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Niblo JK, Swartley JR, Zhang Z, DuBay KH. 2D capsid formation within an oscillatory energy landscape: orderly self-assembly depends on the interplay between a dynamic potential and intrinsic relaxation times. SOFT MATTER 2024. [PMID: 39046256 DOI: 10.1039/d4sm00455h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but investigations thus far have focused on systems of simple colloids or their binary mixtures. In this work, we expand our understanding of the effect of temporally oscillating interactions to a two-dimensional coarse-grained viral capsid-like model that undergoes a self-limited assembly. This model includes multiple intrinsic relaxation times due to the internal structure of the capsid subunits and, under certain interaction regimes, proceeds via a two-step nucleation mechanism. We find that oscillations much faster than the local intrinsic relaxation times can be described via a time averaged inter-particle potential across a wide range of interaction strengths, while oscillations much slower than these relaxation times result in structures that adapt to the attraction strength of the current half-cycle. Interestingly, oscillation periods similar to these relaxation times shift the interaction window over which orderly assembly occurs by enabling error correction during the half-cycles with weaker attractions. Our results provide fundamental insights to non-equilibrium self-assembly on temporally variant energy landscapes.
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Affiliation(s)
- Jessica K Niblo
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Jacob R Swartley
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Zhongmin Zhang
- Department of Chemistry, University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Kateri H DuBay
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
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2
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Lopez-Ceja J, Flores V, Juliano S, Machler S, Smith S, Mansingh G, Shen M, Tanjeem N. Programmable Crowding and Tunable Phases in a Binary Mixture of Colloidal Particles under Light-Driven Thermal Convection. J Phys Chem B 2024. [PMID: 39047259 DOI: 10.1021/acs.jpcb.4c02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We employ photothermally driven self-assembly of colloidal particles to design microscopic structures with programmable size and tunable order. The experimental system is based on a binary mixture of "plasmonic heater" gold nanoparticles and "assembly building block" microparticles. Photothermal heating of the gold nanoparticles under visible light causes a natural convection flow that efficiently assembles the microscale building block particles (diameter 1-10 μm) into a monolayer. We identify the onset of active Brownian motion of colloidal particles under this convective flow by varying the conditions of light intensity, gold nanoparticle concentration, and sample height. We realize a crowded assembly of microparticles around the center of illumination and show that the size of the particle crowd can be programmed using patterned light illumination. In a binary mixture of gold nanoparticles and polystyrene microparticles, we demonstrate the formation of rapid and large-scale crystalline monolayers, covering an area of 0.88 mm2 within 10 min. We find that the structural order of the assembly can be tuned by varying the surface charge of the nanoparticles and the size of the microparticles, giving rise to the formation of different phases-colloidal crystals, crowds, and gels. Using Monte Carlo simulations, we explain how the phases emerge from the interplay between hydrodynamic and electrostatic interactions, as well as the assembly kinetics. Our study demonstrates the promise of self-assembly with programmable shapes and structural order under nonequilibrium conditions using an accessible setup comprising only binary mixtures and LED light.
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Affiliation(s)
- Jose Lopez-Ceja
- Department of Mechanical Engineering, California State University, Fullerton, California 92831, United states
| | - Vanessa Flores
- Department of Mechanical Engineering, California State University, Fullerton, California 92831, United states
| | - Shirlaine Juliano
- Department of Biology, California State University, Fullerton, California 92831, United states
| | - Sean Machler
- Department of Physics, California State University, Fullerton, California 92831, United states
| | - Stephen Smith
- Department of Physics, California State University, Fullerton, California 92831, United states
| | - Gargi Mansingh
- Department of Physics, California State University, Fullerton, California 92831, United states
| | - Meng Shen
- Department of Physics, California State University, Fullerton, California 92831, United states
| | - Nabila Tanjeem
- Department of Physics, California State University, Fullerton, California 92831, United states
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3
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Videbæk TE, Hayakawa D, Grason GM, Hagan MF, Fraden S, Rogers WB. Economical routes to size-specific assembly of self-closing structures. SCIENCE ADVANCES 2024; 10:eado5979. [PMID: 38959303 PMCID: PMC11221488 DOI: 10.1126/sciadv.ado5979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Programmable self-assembly has seen an explosion in the diversity of synthetic crystalline materials, but developing strategies that target "self-limiting" assemblies has remained a challenge. Among these, self-closing structures, in which the local curvature defines the finite global size, are prone to polymorphism due to thermal bending fluctuations, a problem that worsens with increasing target size. Here, we show that assembly complexity can be used to eliminate this source of polymorphism in the assembly of tubules. Using many distinct components, we prune the local density of off-target geometries, increasing the selectivity of the tubule width and helicity to nearly 100%. We further show that by reducing the design constraints to target either the pitch or the width alone, fewer components are needed to reach complete selectivity. Combining experiments with theory, we reveal an economical limit, which determines the minimum number of components required to create arbitrary assembly sizes with full selectivity.
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Affiliation(s)
- Thomas E. Videbæk
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daichi Hayakawa
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - W. Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
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4
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King EM, Du CX, Zhu QZ, Schoenholz SS, Brenner MP. Programming patchy particles for materials assembly design. Proc Natl Acad Sci U S A 2024; 121:e2311891121. [PMID: 38913891 PMCID: PMC11228463 DOI: 10.1073/pnas.2311891121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/21/2023] [Indexed: 06/26/2024] Open
Abstract
Direct design of complex functional materials would revolutionize technologies ranging from printable organs to novel clean energy devices. However, even incremental steps toward designing functional materials have proven challenging. If the material is constructed from highly complex components, the design space of materials properties rapidly becomes too computationally expensive to search. On the other hand, very simple components such as uniform spherical particles are not powerful enough to capture rich functional behavior. Here, we introduce a differentiable materials design model with components that are simple enough to design yet powerful enough to capture complex materials properties: rigid bodies composed of spherical particles with directional interactions (patchy particles). We showcase the method with self-assembly designs ranging from open lattices to self-limiting clusters, all of which are notoriously challenging design goals to achieve using purely isotropic particles. By directly optimizing over the location and interaction of the patches on patchy particles using gradient descent, we dramatically reduce the computation time for finding the optimal building blocks.
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Affiliation(s)
- Ella M King
- Department of Physics, Harvard University, Cambridge, MA 02139
| | - Chrisy Xiyu Du
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02139
- Mechanical Engineering, University of Hawai'i at Mānoa, Honolulu, HI 96822
| | - Qian-Ze Zhu
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02139
| | | | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02139
- Google Research, Mountainview, CA 94043
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5
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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024; 18:14791-14840. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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6
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Duque CM, Hall DM, Tyukodi B, Hagan MF, Santangelo CD, Grason GM. Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra. Proc Natl Acad Sci U S A 2024; 121:e2315648121. [PMID: 38669182 PMCID: PMC11067059 DOI: 10.1073/pnas.2315648121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
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Affiliation(s)
- Carlos M. Duque
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Department of Physics, University of Massachusetts, Amherst, MA01003
| | - Douglas M. Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
| | - Botond Tyukodi
- Department of Physics, Babes-Bolyai University, Cluj-Napoca400084, Romania
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Christian D. Santangelo
- Department of Physics, University of Massachusetts, Amherst, MA01003
- Department of Physics, Syracuse University, Syracuse, NY13210
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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7
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Ramakrishna Y, Naresh M, Mrinalini M, Pravallika N, Kumari P, Bhavani B, Giribabu L, Prasanthkumar S. Narcissistic self-sorting in Zn(II) porphyrin derived semiconducting nanostructures. NANOSCALE 2024. [PMID: 38683187 DOI: 10.1039/d4nr00991f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The narcissistic self-sorted phenomenon is explicitly attributed to the structural similarities in organic molecules. Although such relevant materials are rarely explored, self-sorted structures from macrocyclic π-conjugated-based p- and n-type organic semiconductors facilitate the increase of exciton dissociation and charge separation in bulk heterojunction solar cells. Herein, we report two extended π-conjugated derivatives consisting of zinc-porphyrin-linked benzothiadiazole acting as an acceptor (PB) and anthracene as a donor (PA). Despite having the same porphyrin π-conjugated core in PA and PB, variations in donor and acceptor moieties make the molecular packing form one-dimensional (1D) self-assembled nanofibers via H- and J-type aggregates. Interestingly, a dissimilar aggregate of PA and PB exists as a mixture (PA + PB), promoting narcissistic self-sorted structures. Electrochemical impedance investigation reveals that the electronic characteristics of self-sorting assemblies are influenced by the difference in electrostatic potentials for PA and PB, resulting in a transitional electrical conductivity of 0.14 S cm-1. Therefore, the design of such materials for the fabrication of effective photovoltaics is promoted by these extraordinary self-sorted behaviors in comparable organic π-conjugated molecules.
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Affiliation(s)
- Yelukula Ramakrishna
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
| | - Madarapu Naresh
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
| | - Madoori Mrinalini
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
- Materials Chemistry Department, CSIR-Institute of Minerals and Materials Technology (IMMT), Bhubaneswar - 751 013, Odisha, India
| | - Nagadatta Pravallika
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
| | - Priti Kumari
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
| | - Botta Bhavani
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
| | - Lingamallu Giribabu
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
| | - Seelam Prasanthkumar
- Department of Polymer & Functional Materials, CSIR-Indian Institute of Chemical Technology (IICT), Tarnaka, Hyderabad-500007, Telangana, India.
- Academy of Scientific and Innovation Research (AcSIR), Ghaziabad-201 002, India
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8
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Lei M, Liao H, Wang S, Zhou H, Zhu J, Wan H, Payne GF, Liu C, Qu X. Electro-Sorting Create Heterogeneity: Constructing A Multifunctional Janus Film with Integrated Compositional and Microstructural Gradients for Guided Bone Regeneration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307606. [PMID: 38225697 DOI: 10.1002/advs.202307606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/25/2023] [Indexed: 01/17/2024]
Abstract
Biology remains the envy of flexible soft matter fabrication because it can satisfy multiple functional needs by organizing a small set of proteins and polysaccharides into hierarchical systems with controlled heterogeneity in composition and microstructure. Here, it is reported that controlled, mild electronic inputs (<10 V; <20 min) induce a homogeneous gelatin-chitosan mixture to undergo sorting and bottom-up self-assembly into a Janus film with compositional gradient (i.e., from chitosan-enriched layer to chitosan/gelatin-contained layer) and tunable dense-porous gradient microstructures (e.g., porosity, pore size, and ratio of dense to porous layers). This Janus film performs is shown multiple functions for guided bone regeneration: the integration of compositional and microstructural features confers flexible mechanics, asymmetric properties for interfacial wettability, molecular transport (directional growth factor release), and cellular responses (prevents fibroblast infiltration but promotes osteoblast growth and differentiation). Overall, this work demonstrates the versatility of electrofabrication for the customized manufacturing of functional gradient soft matter.
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Affiliation(s)
- Miao Lei
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haitao Liao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shijia Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hang Zhou
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianwei Zhu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haoran Wan
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Biomedical Device Institute, 5118 A. James Clark Hall, College Park, Maryland, 20742, USA
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
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9
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Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
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Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
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10
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Ciardi M, Cinti F, Pellicane G, Prestipino S. Supersolid Phases of Bosonic Particles in a Bubble Trap. PHYSICAL REVIEW LETTERS 2024; 132:026001. [PMID: 38277582 DOI: 10.1103/physrevlett.132.026001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/06/2023] [Accepted: 12/04/2023] [Indexed: 01/28/2024]
Abstract
Confinement can have a considerable effect on the behavior of particle systems and is therefore an effective way to discover new phenomena. A notable example is a system of identical bosons at low temperature under an external field mimicking an isotropic bubble trap, which constrains the particles to a portion of space close to a spherical surface. Using path integral Monte Carlo simulations, we examine the spatial structure and superfluid fraction in two emblematic cases. First, we look at soft-core bosons, finding the existence of supersolid cluster arrangements with polyhedral symmetry; we show how different numbers of clusters are stabilized depending on the trap radius and the particle mass, and we characterize the temperature behavior of the cluster phases. A detailed comparison with the behavior of classical soft-core particles is provided too. Then, we examine the case, of more immediate experimental interest, of a dipolar condensate on the sphere, demonstrating how a quasi-one-dimensional supersolid of clusters is formed on a great circle for realistic values of density and interaction parameters. Crucially, this supersolid phase is only slightly disturbed by gravity. We argue that the predicted phases can be revealed in magnetic traps with spherical-shell geometry, possibly even in a lab on Earth. Our results pave the way for future simulation studies of correlated quantum systems in curved geometries.
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Affiliation(s)
- Matteo Ciardi
- Dipartimento di Fisica e Astronomia, Università di Firenze, I-50019 Sesto Fiorentino (FI), Italy
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
- INFN, Sezione di Firenze, I-50019 Sesto Fiorentino (FI), Italy
| | - Fabio Cinti
- Dipartimento di Fisica e Astronomia, Università di Firenze, I-50019 Sesto Fiorentino (FI), Italy
- INFN, Sezione di Firenze, I-50019 Sesto Fiorentino (FI), Italy
- Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
| | - Giuseppe Pellicane
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali, Università degli Studi di Messina, I-98125 Messina, Italy
- CNR-IPCF, Viale F. Stagno d'Alcontres, 37-98158, Messina, Italy
- School of Chemistry and Physics, University of Kwazulu-Natal, 3209 Pietermaritzburg, South Africa
- National Institute of Theoretical and Computational Sciences (NIThECS), 3209 Pietermaritzburg, South Africa
| | - Santi Prestipino
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, viale F. Stagno d'Alcontres 31, I-98166 Messina, Italy
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11
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Wang M, Grason G. Thermal stability and secondary aggregation of self-limiting, geometrically frustrated assemblies: Chain assembly of incommensurate polybricks. Phys Rev E 2024; 109:014608. [PMID: 38366461 DOI: 10.1103/physreve.109.014608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/21/2023] [Indexed: 02/18/2024]
Abstract
In geometrically frustrated assemblies, equilibrium self-limitation manifests in the form of a minimum in the free energy per subunit at a finite, multisubunit size which results from the competition between the elastic costs of frustration within an assembly and the surface energy at its boundaries. Physical realizations-from ill-fitting particle assemblies to self-twisting protein superstructures-are capable of multiple mechanisms of escaping the cumulative costs of frustration, resulting in unlimited equilibrium assembly, including elastic modes of "shape flattening" and the formation of weak, defective bonds that screen intra-assembly stresses. Here we study a model of one-dimensional chain assembly of incommensurate "polybricks" and determine its equilibrium assembly as a function of temperature, concentration, degree of shape frustration, elasticity, and interparticle binding, notably focusing on how weakly cohesive, defective bonds give rise to strongly temperature-dependent assembly. Complex assembly behavior derives from the competition between multiple distinct local minima in the free-energy landscape, including self-limiting chains, weakly bound aggregates of self-limiting chains, and strongly bound, elastically defrustrated assemblies. We show that this scenario, in general, gives rise to anomalous multiple aggregation behavior, in which disperse subunits (stable at low concentration and high temperature) first exhibit a primary aggregation transition to self-limiting chains (at intermediate concentration and temperature) which are ultimately unstable to condensation into unlimited assembly of finite-chains through weak binding beyond a secondary aggregation transition (at low temperature and high concentration). We show that window of stable self-limitation is determined both by the elastic costs of frustration in the assembly as well as energetic and entropic features of intersubunit binding.
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Affiliation(s)
- Michael Wang
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Gregory Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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12
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Schönhöfer PWA, Sun K, Mao X, Glotzer SC. Rationalizing Euclidean Assemblies of Hard Polyhedra from Tessellations in Curved Space. PHYSICAL REVIEW LETTERS 2023; 131:258201. [PMID: 38181337 DOI: 10.1103/physrevlett.131.258201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/20/2023] [Indexed: 01/07/2024]
Abstract
Entropic self-assembly is governed by the shape of the constituent particles, yet a priori prediction of crystal structures from particle shape alone is nontrivial for anything but the simplest of space-filling shapes. At the same time, most polyhedra are not space filling due to geometric constraints, but these constraints can be relaxed or even eliminated by sufficiently curving space. We show using Monte Carlo simulations that the majority of hard Platonic solids self-assemble entropically into space-filling crystals when constrained to the surface volume of a 3-sphere. As we gradually decrease curvature to "flatten" space and compare the local morphologies of crystals assembling in curved and flat space, we show that the Euclidean assemblies can be categorized as either remnants of tessellations in curved space (tetrahedra and dodecahedra) or nontessellation-based assemblies caused by large-scale geometric frustration (octahedra and icosahedra).
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Affiliation(s)
- Philipp W A Schönhöfer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kai Sun
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoming Mao
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sharon C Glotzer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Sun JH, Plummer A, Zhang GH, Nelson DR, Manoharan VN. Geometric frustration of hard-disk packings on cones. Phys Rev E 2023; 108:054608. [PMID: 38115492 DOI: 10.1103/physreve.108.054608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 12/21/2023]
Abstract
Conical surfaces pose an interesting challenge to crystal growth: A crystal growing on a cone can wrap around and meet itself at different radii. We use a disk-packing algorithm to investigate how this closure constraint can geometrically frustrate the growth of single crystals on cones with small opening angles. By varying the crystal seed orientation and cone angle, we find that-except at special commensurate cone angles-crystals typically form a seam that runs along the axial direction of the cone, while near the tip, a disordered particle packing forms. We show that the onset of disorder results from a finite-size effect that depends strongly on the circumference and not on the seed orientation or cone angle. This finite-size effect occurs also on cylinders, and we present evidence that on both cylinders and cones, the defect density increases exponentially as circumference decreases. We introduce a simple model for particle attachment at the seam that explains the dependence on the circumference. Our findings suggest that the growth of single crystals can become frustrated even very far from the tip when the cone has a small opening angle. These results may provide insights into the observed geometry of conical crystals in biological and materials applications.
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Affiliation(s)
- Jessica H Sun
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Abigail Plummer
- Princeton Center for Complex Materials, Princeton University, Princeton, New Jersey 08540, USA
| | - Grace H Zhang
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David R Nelson
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Vinothan N Manoharan
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA and Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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14
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Das A, Limmer DT. Nonequilibrium design strategies for functional colloidal assemblies. Proc Natl Acad Sci U S A 2023; 120:e2217242120. [PMID: 37748070 PMCID: PMC10556551 DOI: 10.1073/pnas.2217242120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 08/17/2023] [Indexed: 09/27/2023] Open
Abstract
We use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.
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Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, CA94720
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, CA94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Kavli Energy NanoSciences Institute, University of California, Berkeley, CA94720
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15
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Hagan MF, Mohajerani F. Self-assembly coupled to liquid-liquid phase separation. PLoS Comput Biol 2023; 19:e1010652. [PMID: 37186597 PMCID: PMC10212142 DOI: 10.1371/journal.pcbi.1010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/25/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Affiliation(s)
- Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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16
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Alekseevskaya AA, Vasilieva EV, Filippov AV, Vasiliev MM, Petrov OF. Isotropic and Anisotropic Monolayer Structures in RF Discharge Plasma. Molecules 2023; 28:molecules28073259. [PMID: 37050022 PMCID: PMC10096438 DOI: 10.3390/molecules28073259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
We present the results of an experimental and analytical study of the structural and dynamic properties of a monolayer consisting of dust grains in an electrostatic trap in an RF discharge plasma. The possibility of forming a monolayer with an isotropic distribution for interparticle distance and kinetic energy of particles in the structure has been experimentally shown. Isotropy has crucial importance for the study of various processes in such systems, including the kinetics of phase transitions, the formation of directed flows, wave propagation, and others.
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Affiliation(s)
- Anastasiya A Alekseevskaya
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya St. 13 Bld. 2, Moscow 125412, Russia
| | - Elena V Vasilieva
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya St. 13 Bld. 2, Moscow 125412, Russia
| | - Anatoly V Filippov
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya St. 13 Bld. 2, Moscow 125412, Russia
- Troitsk Institute for Innovation and Fusion Research, Pushkovykh St., vl. 12, Troitsk 108840, Russia
| | - Mikhail M Vasiliev
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya St. 13 Bld. 2, Moscow 125412, Russia
| | - Oleg F Petrov
- Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya St. 13 Bld. 2, Moscow 125412, Russia
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17
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Matarranz B, Díaz‐Cabrera S, Ghosh G, Carreira‐Barral I, Soberats B, García‐Valverde M, Quesada R, Fernández G. Anticooperative Supramolecular Oligomerization Mediated by V‐Shaped Monomer Design and Unconventional Hydrogen Bonds. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202218555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Beatriz Matarranz
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 36 48149 Münster Germany
| | - Sandra Díaz‐Cabrera
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Goutam Ghosh
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 36 48149 Münster Germany
| | | | - Bartolome Soberats
- Department of Chemistry, Universitat de les Illes Balears Cra. Valldemossa, Km. 7.5 07122 Palma de Mallorca Spain
| | - María García‐Valverde
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Roberto Quesada
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Gustavo Fernández
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 36 48149 Münster Germany
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18
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Gomez Melo S, Wörthmüller D, Gönczy P, Banterle N, Schwarz US. Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface. J Chem Phys 2023; 158:085102. [PMID: 36859084 DOI: 10.1063/5.0135349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The Spindle Assembly Abnormal Protein 6 (SAS-6) forms dimers, which then self-assemble into rings that are critical for the nine-fold symmetry of the centriole organelle. It has recently been shown experimentally that the self-assembly of SAS-6 rings is strongly facilitated on a surface, shifting the reaction equilibrium by four orders of magnitude compared to the bulk. Moreover, a fraction of non-canonical symmetries (i.e., different from nine) was observed. In order to understand which aspects of the system are relevant to ensure efficient self-assembly and selection of the nine-fold symmetry, we have performed Brownian dynamics computer simulation with patchy particles and then compared our results with the experimental ones. Adsorption onto the surface was simulated by a grand canonical Monte Carlo procedure and random sequential adsorption kinetics. Furthermore, self-assembly was described by Langevin equations with hydrodynamic mobility matrices. We find that as long as the interaction energies are weak, the assembly kinetics can be described well by coagulation-fragmentation equations in the reaction-limited approximation. By contrast, larger interaction energies lead to kinetic trapping and diffusion-limited assembly. We find that the selection of nine-fold symmetry requires a small value for the angular interaction range. These predictions are confirmed by the experimentally observed reaction constant and angle fluctuations. Overall, our simulations suggest that the SAS-6 system works at the crossover between a relatively weak binding energy that avoids kinetic trapping and a small angular range that favors the nine-fold symmetry.
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Affiliation(s)
- Santiago Gomez Melo
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
| | - Dennis Wörthmüller
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Niccolo Banterle
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Ulrich S Schwarz
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany
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19
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Matarranz B, Díaz-Cabrera S, Ghosh G, Carreira-Barral I, Soberats B, García-Valverde M, Quesada R, Fernández G. Anticooperative Supramolecular Oligomerization Mediated by V-Shaped Monomer Design and Unconventional Hydrogen Bonds. Angew Chem Int Ed Engl 2023; 62:e202218555. [PMID: 36828774 DOI: 10.1002/anie.202218555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 02/26/2023]
Abstract
After more than three decades of extensive investigations on supramolecular polymers, strategies for self-limiting growth still remain challenging. Herein, we exploit a new V-shaped monomer design to achieve anticooperatively formed oligomers with superior robustness and high luminescence. In toluene, the monomer-oligomer equilibrium is shifted to the monomer side, enabling the elucidation of the molecular packing modes and the resulting (weak) anticooperativity. Steric effects associated with an antiparallel staircase organization of the dyes are proposed to outcompete aromatic and unconventional B-F⋅⋅⋅H-N/C interactions, restricting the growth at the stage of oligomers. In methylcyclohexane (MCH), the packing modes and the anticooperativity are preserved; however, pronounced solvophobic and chain-enwrapping effects lead to thermally ultrastable oligomers. Our results shed light on understanding anticooperative effects and restricted growth in self-assembly.
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Affiliation(s)
- Beatriz Matarranz
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
| | - Sandra Díaz-Cabrera
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Goutam Ghosh
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
| | - Israel Carreira-Barral
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Bartolome Soberats
- Department of Chemistry, Universitat de les Illes Balears Cra., Valldemossa, Km. 7.5, 07122, Palma de Mallorca, Spain
| | - María García-Valverde
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Roberto Quesada
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Gustavo Fernández
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany
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20
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Hall DM, Stevens MJ, Grason GM. Building blocks of non-Euclidean ribbons: size-controlled self-assembly via discrete frustrated particles. SOFT MATTER 2023; 19:858-881. [PMID: 36636841 DOI: 10.1039/d2sm01371a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current challenge is to understand the connection between microscopic physical properties of misfitting "building blocks" and emergent assembly behavior at the mesoscale. We present and analyze a particle-based description of what is arguably the best studied example for frustrated soft matter assembly, negative-curvature ribbon assembly, observed in both assemblies of chiral surfactants and shape-frustrated nanoparticles. Based on our particle model, known as saddle wedge monomers, we numerically test the connection between microscopic shape and interactions of the misfitting subunits and the emergent behavior at the supra-particle scale, specifically focussing on the propagation and relaxation of inter-particle strains, the emergent role of extrinsic shape on frustrated ribbons and the equilibrium regime of finite width selection. Beyond the intuitive role of shape misfit, we show that self-limitation is critically dependent on the finite range of cohesive interactions, with larger size finite assemblies requiring increasing short-range interparticle forces. Additionally, we demonstrate that non-linearities arising from discrete particle interactions alter self-limiting behavior due to both strain-softening in shape-flattened assembly and partial yielding of highly strained bonds, which in turn may give rise to states of hierarchical, multidomain assembly. Tracing the regimes of frustration-limited assembly to the specific microscopic features of misfitting particle shapes and interactions provides necessary guidance for translating the theory of size-programmable assembly into design of intentionally-frustrated colloidal particles.
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Affiliation(s)
- Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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21
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Long C, Selinger JV. Explicit demonstration of geometric frustration in chiral liquid crystals. SOFT MATTER 2023; 19:519-529. [PMID: 36541414 DOI: 10.1039/d2sm01420c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Many solid materials and liquid crystals exhibit geometric frustration, meaning that they have an ideal local structure that cannot fill up space. For that reason, the global phase must be a compromise between the ideal local structure and geometric constraints. As an explicit example of geometric frustration, we consider a chiral liquid crystal confined in a long cylinder with free boundaries. When the radius of the tube is sufficiently small, the director field forms a double-twist configuration, which is the ideal local structure. However, when the radius becomes larger (compared with the natural twist of the liquid crystal), the double-twist structure cannot fill space, and hence the director field must transform into some other chiral structure that can fill space. This space-filling structure may be either (1) a cholesteric phase with single twist, or (2) a set of double-twist regions separated by a disclination, which can be regarded as the beginning of a blue phase. We investigate these structures using theory and simulations, and show how the relative free energies depend on the system size, the natural twist, and the disclination energy. As another example, we also study a cholesteric liquid crystal confined between two infinite parallel plates with free boundaries.
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Affiliation(s)
- Cheng Long
- Department of Physics, Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA.
| | - Jonathan V Selinger
- Department of Physics, Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA.
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22
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Geometrically programmed self-limited assembly of tubules using DNA origami colloids. Proc Natl Acad Sci U S A 2022; 119:e2207902119. [PMID: 36252043 PMCID: PMC9618141 DOI: 10.1073/pnas.2207902119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature is replete with self-assembled materials that have one or more self-limited dimensions, including shells, tubules, and fibers. Despite significant advances in making nanometer- and micrometer-scale subunits, the programmable assembly of similar self-limiting architectures from synthetic components has remained largely out of reach. In this article, we create geometrically programmed subunits using DNA origami and study their assembly into tubules with a self-limited width. We show that the average self-limited dimension can be tuned by changing the local curvature encoded in a single subunit. Exploiting the programmability of our system, we further test the tradeoffs between fidelity and complexity embodied by two paradigms for self-limited assembly: self-closure through programmed curvature and addressable assembly through programmed specific interactions. Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.
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23
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Fang H, Tyukodi B, Rogers WB, Hagan MF. Polymorphic self-assembly of helical tubules is kinetically controlled. SOFT MATTER 2022; 18:6716-6728. [PMID: 36039801 PMCID: PMC9472595 DOI: 10.1039/d2sm00679k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly. In this article, we study an example class of self-closing assemblies: cylindrical tubules that assemble from triangular monomers. By combining kinetic Monte Carlo simulations, free energy calculations, and simple theoretical models, we show that a range of programmable size scales can be targeted by controlling the intricate balance between the preferred curvature of the monomers and their interaction strengths. However, their assembly is kinetically controlled-the tubule morphology is essentially fixed shortly after closure, resulting in a distribution of tubule widths that is significantly broader than the equilibrium distribution. We develop a simple kinetic model based on this observation and the underlying free-energy landscape of assembling tubules that quantitatively describes the distributions. Our results are consistent with recent experimental observations of tubule assembly from triangular DNA origami monomers. The modeling framework elucidates design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality.
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Affiliation(s)
- Huang Fang
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
- Department of Physics, Babes-Bolyai University, 400084 Cluj-Napoca, Romania
| | - W Benjamin Rogers
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
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24
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Tyukodi B, Mohajerani F, Hall DM, Grason GM, Hagan MF. Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries. ACS NANO 2022; 16:9077-9085. [PMID: 35638478 PMCID: PMC10362403 DOI: 10.1021/acsnano.2c00865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration. The results determine the parameter range where finite-temperature self-limiting assembly occurs, in which the equilibrium assembly size distribution is sharply peaked around a well-defined finite size. The simulations also identify two mechanisms by which the system can escape frustration and assemble to unlimited size, and determine the particle-scale properties of subunits that suppress unbounded growth.
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Affiliation(s)
- Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Farzaneh Mohajerani
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
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25
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Yang X, Lu ZY. Nanoparticle cluster formation mechanisms elucidated via Markov state modeling: Attraction range effects, aggregation pathways, and counterintuitive transition rates. J Chem Phys 2022; 156:214902. [DOI: 10.1063/5.0086110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanoparticle clusters are promising candidates for developing functional materials. However, it is still a challenging task to fabricate them in a predictable and controllable way, which requires investigation of the possible mechanisms underlying cluster formation at the nanoscale. By constructing Markov state models (MSMs) at the microstate level, we find that for highly dispersed particles to form a highly aggregated cluster, there are multiple coexisting pathways, which correspond to direct aggregation, or pathways that need to pass through partially aggregated, intermediate states. Varying the range of attraction between nanoparticles is found to significantly affect pathways. As the attraction range becomes narrower, compared to direct aggregation, some pathways that need to pass through partially aggregated intermediate states become more competitive. In addition, from MSMs constructed at the macrostate level, the aggregation rate is found to be counterintuitively lower with a lower free-energy barrier, which is also discussed.
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Affiliation(s)
- Xi Yang
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
| | - Zhong-Yuan Lu
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
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26
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Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. J Chem Phys 2022; 156:194902. [PMID: 35597653 DOI: 10.1063/5.0087769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.
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Affiliation(s)
- Ivan Palaia
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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27
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Helmers I, Hossain MS, Bäumer N, Wesarg P, Soberats B, Shimizu LS, Fernández G. Anti-cooperative Self-Assembly with Maintained Emission Regulated by Conformational and Steric Effects. Angew Chem Int Ed Engl 2022; 61:e202200390. [PMID: 35112463 PMCID: PMC9311066 DOI: 10.1002/anie.202200390] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Indexed: 12/28/2022]
Abstract
Herein, we present a strategy to enable a maintained emissive behavior in the self‐assembled state by enforcing an anti‐cooperative self‐assembly involving weak intermolecular dye interactions. To achieve this goal, we designed a conformationally flexible monomer unit 1 with a central 1,3‐substituted (diphenyl)urea hydrogen bonding synthon that is tethered to two BODIPY dyes featuring sterically bulky trialkoxybenzene substituents at the meso‐position. The competition between attractive forces (H‐bonding and aromatic interactions) and destabilizing effects (steric and competing conformational effects) limits the assembly, halting the supramolecular growth at the stage of small oligomers. Given the presence of weak dye–dye interactions, the emission properties of molecularly dissolved 1 are negligibly affected upon aggregation. Our findings contribute to broadening the scope of emissive supramolecular assemblies and controlled supramolecular polymerization.
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Affiliation(s)
- Ingo Helmers
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Muhammad Saddam Hossain
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Nils Bäumer
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Paul Wesarg
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Bartolome Soberats
- Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, 07122, Palma de Mallorca, Spain
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Gustavo Fernández
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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28
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Wong CK, Tang C, Schreck JS, Doye JPK. Characterizing the free-energy landscapes of DNA origamis. NANOSCALE 2022; 14:2638-2648. [PMID: 35129570 DOI: 10.1039/d1nr05716b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the strong bending of DNA nanotubes and the potentially bistable landscape of twisted DNA origami sheets. The homogeneous bending of the DNA nanotubes is well described by the worm-like chain model; for more extreme bending the nanotubes reversibly buckle with the bending deformations localized at one or two "kinks". For a twisted one-layer DNA origami, the twist is coupled to the bending of the sheet giving rise to a free-energy landscape that has two nearly-degenerate minima that have opposite curvatures. By contrast, for a two-layer origami, the increased stiffness with respect to bending leads to a landscape with a single free-energy minimum that has a saddle-like geometry. The ability to compute such landscapes is likely to be particularly useful for DNA mechanotechnology and for understanding stress accumulation during the self-assembly of origamis into higher-order structures.
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Affiliation(s)
- Chak Kui Wong
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Chuyan Tang
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - John S Schreck
- National Center for Atmospheric Research, Computational and Information Systems Laboratory, 850 Table Mesa Drive, Boulder, CO 80305, USA
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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29
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Helmers I, Hossain MS, Bäumer N, Wesarg P, Soberats B, Shimizu LS, Fernandez G. Anti‐cooperative Self‐Assembly with Maintained Emission Regulated by Conformational and Steric Effects. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ingo Helmers
- WWU Münster: Westfalische Wilhelms-Universitat Munster Organisch-Chemisches Institut GERMANY
| | | | - Nils Bäumer
- WWU Münster: Westfalische Wilhelms-Universitat Munster Organisch-Chemisches Institut GERMANY
| | - Paul Wesarg
- WWU Münster: Westfalische Wilhelms-Universitat Munster Organisch-Chemisches Institut GERMANY
| | - Bartolome Soberats
- Universitat de les Illes Balears Facultat de Ciencies Quimica Organica SPAIN
| | - Linda S. Shimizu
- University of South Carolina Chemistry and Biochemistry UNITED STATES
| | - Gustavo Fernandez
- WWU Münster Organisch-Chemisches Institut Correnstraße, 4ß 48149 Münster GERMANY
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30
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Meiri S, Efrati E. Cumulative geometric frustration and superextensive energy scaling in a nonlinear classical XY-spin model. Phys Rev E 2022; 105:024703. [PMID: 35291144 DOI: 10.1103/physreve.105.024703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Geometric frustration results from a discrepancy between the locally favored arrangement of the constituents of a system and the geometry of the embedding space. Geometric frustration can be either noncumulative, which implies an extensive energy growth, or cumulative, which implies superextensive energy scaling and highly cooperative ground-state configurations which may depend on the dimensions of the system. Cumulative geometric frustration was identified in a variety of continuous systems including liquid crystals, filament bundles, and molecular crystals. However, a spin-lattice model which clearly demonstrates cumulative geometric frustration was lacking. In this paper we describe a nonlinear variation of the XY-spin model on a triangular lattice that displays cumulative geometric frustration. The model is studied numerically and analyzed in three distinct parameter regimes, which are associated with different energy minimizing configurations. We show that, despite the difference in the ground-state structure in the different regimes, in all cases the superextensive power-law growth of the frustration energy for small domains grows with the same universal exponent that is predicted from the structure of the underlying compatibility condition.
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Affiliation(s)
- Snir Meiri
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Abstract
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatics interaction between the positive charges on capsid proteins and the negative charges on the genome. Despite its importance and many decades of intense research, how the virus selects and packages its native RNA inside the crowded environment of a host cell cytoplasm in the presence of an abundance of nonviral RNA and other anionic polymers has remained a mystery. In this paper, we perform a series of simulations to monitor the growth of viral shells and find the mechanism by which cargo-coat protein interactions can impact the structure and stability of the viral shells. We show that coat protein subunits can assemble around a globular nucleic acid core by forming nonicosahedral cages, which have been recently observed in assembly experiments involving small pieces of RNA. We find that the resulting cages are strained and can easily be split into fragments along stress lines. This suggests that such metastable nonicosahedral intermediates could be easily reassembled into the stable native icosahedral shells if the larger wild-type genome becomes available, despite the presence of a myriad of nonviral RNAs.
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Affiliation(s)
- Sanaz Panahandeh
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
| | - Siyu Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, United States
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32
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Videbæk TE, Fang H, Hayakawa D, Tyukodi B, Hagan MF, Rogers WB. Tiling a tubule: how increasing complexity improves the yield of self-limited assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:10.1088/1361-648X/ac47dd. [PMID: 34983038 PMCID: PMC8857047 DOI: 10.1088/1361-648x/ac47dd] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of systems with self-limited length scales is that thermal fluctuations can lead to the assembly of nearby, off-target states. We investigate strategies for limiting off-target assembly by using multiple types of subunits. Using simulations and energetics calculations, we explore this concept by considering the assembly of tubules built from triangular subunits that bind edge to edge. While in principle, a single type of triangle can assemble into tubules with a monodisperse width distribution, in practice, the finite bending rigidity of the binding sites leads to the formation of off-target structures. To increase the assembly specificity, we introduce tiling rules for assembling tubules from multiple species of triangles. We show that the selectivity of the target structure can be dramatically improved by using multiple species of subunits, and provide a prescription for choosing the minimum number of subunit species required for near-perfect yield. Our approach of increasing the system's complexity to reduce the accessibility of neighboring structures should be generalizable to other systems beyond the self-assembly of tubules.
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Affiliation(s)
- Thomas E. Videbæk
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
| | - Huang Fang
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
| | - Daichi Hayakawa
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
| | - Botond Tyukodi
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
| | - W. Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, USA
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33
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Meiri S, Efrati E. Cumulative geometric frustration in physical assemblies. Phys Rev E 2021; 104:054601. [PMID: 34942847 DOI: 10.1103/physreve.104.054601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 10/13/2021] [Indexed: 11/07/2022]
Abstract
Geometric frustration arises whenever the constituents of a physical assembly locally favor an arrangement that cannot be realized globally. Recently, such frustrated assemblies were shown to exhibit filamentation, size limitation, large morphological variations and other exotic response properties. While these unique characteristics can be shown to be a direct outcome of the geometric frustration, some geometrically frustrated systems do not exhibit any of the above phenomena. In this work we exploit the intrinsic approach to provide a framework for directly addressing the frustration in physical assemblies. The framework highlights the role of the compatibility conditions associated with the intrinsic fields describing the physical assembly. We show that the structure of the compatibility conditions determines the behavior of small assemblies and in particular predicts their superextensive energy growth exponent. We illustrate the use of this framework to several well-known frustrated assemblies.
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Affiliation(s)
- Snir Meiri
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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34
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Kuyyamudi C, Menon SN, Casares F, Sinha S. Disorder in cellular packing can alter proliferation dynamics to regulate growth. Phys Rev E 2021; 104:L052401. [PMID: 34942790 DOI: 10.1103/physreve.104.l052401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022]
Abstract
The mechanisms by which an organ regulates its growth are not yet fully understood, especially when the cells are closely packed as in epithelial tissues. We explain growth arrest as a collective dynamical transition in coupled oscillators on disordered lattices. As the cellular morphologies become homogeneous over the course of development, the signals induced by cell-cell contact increase beyond a critical value that triggers coordinated cessation of the cell-cycle oscillators driving cell division. Thus, control of cell proliferation is causally related to the geometry of cellular packing.
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Affiliation(s)
- Chandrashekar Kuyyamudi
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
| | - Fernando Casares
- CABD, CSIC-Universidad Pablo de Olavide-JA, 41013 Seville, Spain
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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35
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Liang Y, Xiang D, Hou Y, Li G, Feng S, Yang M. Size-encoded hierarchical self-assembly of nanoparticles into chains and tubules. J Colloid Interface Sci 2021; 604:866-875. [PMID: 34303886 DOI: 10.1016/j.jcis.2021.07.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
Hierarchical structures with sophisticated patterns allow the emergence of challenging properties. However, the highly cooperative and specific interactions needed for assembly spanning different length scales are typically lacking in inorganic nanoparticles (NPs). Here we show that size can be a common structural driving force for controlling hierarchical assembly of inorganic NPs into anisotropic superstructures. It involves first the self-limiting assembly of small CdS NPs into large supraparticles and their subsequent spontaneous organization into chains and tubules hundreds of nanometers long. Our quantitative calculations based on DLVO theory reveals an intrinsic size effect relating to the dimension change of assembly units in accordance with a negative cooperativity. It is shown that the size increase in building blocks creates an effective kinetic barrier contrast at different attachment sites due to the increase of interparticle electrostatic repulsion, switching the assembly from thermodynamically preferred 3D to kinetically favored 1D pathway. The size-encoded hierarchical assembly is accompanied by the ligand-controlled Oswald ripening process, which is responsible for the variation of hierarchical patterns from chains to tubules. The general principle in governing multistage inorganic NP ordering represents an important guideline toward the complex mesoscale structures that may surpass traditional materials in both design and functionality.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China; Key Laboratory of Microsystems and Micronanostructures Manufacturing, Harbin Institute of Technology 2 Yikuang Street, Harbin 150080, PR China
| | - Di Xiang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China; Key Laboratory of Microsystems and Micronanostructures Manufacturing, Harbin Institute of Technology 2 Yikuang Street, Harbin 150080, PR China
| | - Ying Hou
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China
| | - Guangshe Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Ming Yang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
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36
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Peterson MSE, Baskaran A, Hagan MF. Vesicle shape transformations driven by confined active filaments. Nat Commun 2021; 12:7247. [PMID: 34903731 PMCID: PMC8668962 DOI: 10.1038/s41467-021-27310-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/12/2021] [Indexed: 12/02/2022] Open
Abstract
In active matter systems, deformable boundaries provide a mechanism to organize internal active stresses. To study a minimal model of such a system, we perform particle-based simulations of an elastic vesicle containing a collection of polar active filaments. The interplay between the active stress organization due to interparticle interactions and that due to the deformability of the confinement leads to a variety of filament spatiotemporal organizations that have not been observed in bulk systems or under rigid confinement, including highly-aligned rings and caps. In turn, these filament assemblies drive dramatic and tunable transformations of the vesicle shape and its dynamics. We present simple scaling models that reveal the mechanisms underlying these emergent behaviors and yield design principles for engineering active materials with targeted shape dynamics.
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Affiliation(s)
- Matthew S E Peterson
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States
| | - Aparna Baskaran
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
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37
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Nguyen TD, Jiménez-Ángeles F, Olvera de la Cruz M. Probing the size-dependent polarizability of mesoscopic ionic clusters and their induced-dipole interactions. J Chem Phys 2021; 155:194901. [PMID: 34800942 DOI: 10.1063/5.0064267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mesoscopic clusters composed of oppositely charged particles are ubiquitous in synthetic and biological soft materials. The effective interaction between these clusters is influenced by their polarizability, that is, the ability of their constituent charges to re-arrange in response to an external electrical field. Here, using coarse-grained simulations, we show that the polarizability of electrically neutral ionic clusters decreases as the number of constituent charges increases and/or their Coulombic interaction strength increases for various ion valencies, ion densities, and degrees of cluster boundary hardness. For clusters of random ionomers and their counterions, their polarizability is shown to depend on the number of polymer chains. The variation of the cluster polarizability with the cluster size indicates that throughout the assembly, the induced-dipole interactions between the clusters may be reduced substantially as they acquire more charges while maintaining zero net charge. Under certain conditions, the induced-dipole interactions may become repulsive, as inferred from our simulations with a polarizable solvent. As a result, the dipole-induced related interactions can serve as a counterbalancing force that contributes to the self-limiting aggregation of charge-containing assemblies.
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Affiliation(s)
- Trung Dac Nguyen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Felipe Jiménez-Ángeles
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Monica Olvera de la Cruz
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
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38
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Charbonneau P, Tarzia M. Solution of disordered microphases in the Bethe approximation. J Chem Phys 2021; 155:024501. [PMID: 34266261 DOI: 10.1063/5.0052111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The periodic microphases that self-assemble in systems with competing short-range attractive and long-range repulsive (SALR) interactions are structurally both rich and elegant. Significant theoretical and computational efforts have thus been dedicated to untangling their properties. By contrast, disordered microphases, which are structurally just as rich but nowhere near as elegant, have not been as carefully considered. Part of the difficulty is that simple mean-field descriptions make a homogeneity assumption that washes away all of their structural features. Here, we study disordered microphases by exactly solving a SALR model on the Bethe lattice. By sidestepping the homogenization assumption, this treatment recapitulates many of the key structural regimes of disordered microphases, including particle and void cluster fluids as well as gelation. This analysis also provides physical insight into the relationship between various structural and thermal observables, between criticality and physical percolation, and between glassiness and microphase ordering.
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Affiliation(s)
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France
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