1
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Shankar S, Scharrer LVD, Bowick MJ, Marchetti MC. Design rules for controlling active topological defects. Proc Natl Acad Sci U S A 2024; 121:e2400933121. [PMID: 38748571 PMCID: PMC11127047 DOI: 10.1073/pnas.2400933121] [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: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 05/27/2024] Open
Abstract
Topological defects play a central role in the physics of many materials, including magnets, superconductors, and liquid crystals. In active fluids, defects become autonomous particles that spontaneously propel from internal active stresses and drive chaotic flows stirring the fluid. The intimate connection between defect textures and active flow suggests that properties of active materials can be engineered by controlling defects, but design principles for their spatiotemporal control remain elusive. Here, we propose a symmetry-based additive strategy for using elementary activity patterns, as active topological tweezers, to create, move, and braid such defects. By combining theory and simulations, we demonstrate how, at the collective level, spatial activity gradients act like electric fields which, when strong enough, induce an inverted topological polarization of defects, akin to a negative susceptibility dielectric. We harness this feature in a dynamic setting to collectively pattern and transport interacting active defects. Our work establishes an additive framework to sculpt flows and manipulate active defects in both space and time, paving the way to design programmable active and living materials for transport, memory, and logic.
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Affiliation(s)
- Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA02138
- Department of Physics, University of Michigan, Ann Arbor, MI48109
| | - Luca V. D. Scharrer
- Department of Physics, University of California, Santa Barbara, CA93106
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Mark J. Bowick
- Department of Physics, University of California, Santa Barbara, CA93106
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA93106
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2
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Liu H, Matthies M, Russo J, Rovigatti L, Narayanan RP, Diep T, McKeen D, Gang O, Stephanopoulos N, Sciortino F, Yan H, Romano F, Šulc P. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024; 384:776-781. [PMID: 38753798 DOI: 10.1126/science.adl5549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
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Affiliation(s)
- Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Thong Diep
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Flavio Romano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30171 Venezia-Mestre, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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3
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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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4
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Evans CG, O'Brien J, Winfree E, Murugan A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 2024; 625:500-507. [PMID: 38233621 PMCID: PMC10794147 DOI: 10.1038/s41586-023-06890-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles1-3. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks4-7. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems.
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Affiliation(s)
- Constantine Glen Evans
- California Institute of Technology, Pasadena, CA, USA.
- Evans Foundation for Molecular Medicine, Pasadena, CA, USA.
- Maynooth University, Maynooth, Ireland.
| | | | - Erik Winfree
- California Institute of Technology, Pasadena, CA, USA.
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5
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McCaskill JS, Karnaushenko D, Zhu M, Schmidt OG. Microelectronic Morphogenesis: Smart Materials with Electronics Assembling into Artificial Organisms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2306344. [PMID: 37814374 DOI: 10.1002/adma.202306344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/27/2023] [Indexed: 10/11/2023]
Abstract
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape materials and their functions in three dimensions to form smart microdevices and microrobots. Electronic information that controls morphology is inheritable like its biological counterpart, genetic information, and is set to open new vistas of technology leading to artificial organisms when coupled with modular design and self-assembly that can make reversible microscopic electrical connections. Three core capabilities of cells in organisms, self-maintenance (homeostatic metabolism utilizing free energy), self-containment (distinguishing self from nonself), and self-reproduction (cell division with inherited properties), once well out of reach for technology, are now within the grasp of information-directed materials. Construction-aware electronics can be used to proof-read and initiate game-changing error correction in microelectronic self-assembly. Furthermore, noncontact communication and electronically supported learning enable one to implement guided self-assembly and enhance functionality. Here, the fundamental breakthroughs that have opened the pathway to this prospective path are reviewed, the extent and way in which the core properties of life can be addressed are analyzed, and the potential and indeed necessity of such technology for sustainable high technology in society is discussed.
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Affiliation(s)
- John S McCaskill
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09126, Chemnitz, Germany
- European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Venice, 30123, Italy
| | - Daniil Karnaushenko
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09126, Chemnitz, Germany
| | - Minshen Zhu
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09126, Chemnitz, Germany
| | - Oliver G Schmidt
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09126, Chemnitz, Germany
- European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Venice, 30123, Italy
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6
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Förste S, Vonshak O, Daube SS, Bar-Ziv RH, Lipowsky R, Rudorf S. Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. Microb Cell Fact 2023; 22:244. [PMID: 38037098 PMCID: PMC10688499 DOI: 10.1186/s12934-023-02237-5] [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: 07/06/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system's three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.
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Affiliation(s)
- Stefanie Förste
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Ohad Vonshak
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shirley S Daube
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Roy H Bar-Ziv
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Sophia Rudorf
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, 30419, Hannover, Germany.
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7
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Parikka JM, Järvinen H, Sokołowska K, Ruokolainen V, Markešević N, Natarajan AK, Vihinen-Ranta M, Kuzyk A, Tapio K, Toppari JJ. Creation of ordered 3D tubes out of DNA origami lattices. NANOSCALE 2023; 15:7772-7780. [PMID: 37057647 DOI: 10.1039/d2nr06001a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.
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Affiliation(s)
- Johannes M Parikka
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Heini Järvinen
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Karolina Sokołowska
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Visa Ruokolainen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Nemanja Markešević
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Maija Vihinen-Ranta
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Kosti Tapio
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - J Jussi Toppari
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
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8
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Cho Y, Jacobs WM. Tuning Nucleation Kinetics via Nonequilibrium Chemical Reactions. PHYSICAL REVIEW LETTERS 2023; 130:128203. [PMID: 37027881 DOI: 10.1103/physrevlett.130.128203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities between liquid-liquid phase separation in these systems, the extent to which the phase-separation kinetics differ remains unclear. Here we show that inhomogeneous chemical reactions can alter the nucleation kinetics of liquid-liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introducing a nonequilibrium interfacial tension. We identify conditions under which nucleation can be accelerated without changing the energetics or supersaturation, thus breaking the correlation between fast nucleation and strong driving forces that is typical of phase separation and self-assembly at thermal equilibrium.
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Affiliation(s)
- Yongick Cho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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9
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Trubiano A, Hagan MF. Optimization of non-equilibrium self-assembly protocols using Markov state models. J Chem Phys 2022; 157:244901. [PMID: 36586982 PMCID: PMC9788858 DOI: 10.1063/5.0130407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
The promise of self-assembly to enable the bottom-up formation of materials with prescribed architectures and functions has driven intensive efforts to uncover rational design principles for maximizing the yield of a target structure. Yet, despite many successful examples of self-assembly, ensuring kinetic accessibility of the target structure remains an unsolved problem in many systems. In particular, long-lived kinetic traps can result in assembly times that vastly exceed experimentally accessible timescales. One proposed solution is to design non-equilibrium assembly protocols in which system parameters change over time to avoid such kinetic traps. Here, we develop a framework to combine Markov state model (MSM) analysis with optimal control theory to compute a time-dependent protocol that maximizes the yield of the target structure at a finite time. We present an adjoint-based gradient descent method that, in conjunction with MSMs for a system as a function of its control parameters, enables efficiently optimizing the assembly protocol. We also describe an interpolation approach to significantly reduce the number of simulations required to construct the MSMs. We demonstrate our approach with two examples; a simple semi-analytic model for the folding of a polymer of colloidal particles, and a more complex model for capsid assembly. Our results show that optimizing time-dependent protocols can achieve significant improvements in the yields of selected structures, including equilibrium free energy minima, long-lived metastable structures, and transient states.
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Affiliation(s)
- Anthony Trubiano
- 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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10
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Bone RA, Sharpe DJ, Wales DJ, Green JR. Stochastic paths controlling speed and dissipation. Phys Rev E 2022; 106:054151. [PMID: 36559408 DOI: 10.1103/physreve.106.054151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Natural processes occur in a finite amount of time and dissipate energy, entropy, and matter. Near equilibrium, thermodynamic intuition suggests that fast irreversible processes will dissipate more energy and entropy than slow quasistatic processes connecting the same initial and final states. For small systems, recently discovered thermodynamic speed limits suggest that faster processes will dissipate more than slower processes. Here, we test the hypothesis that this relationship between speed and dissipation holds for stochastic paths far from equilibrium. To analyze stochastic paths on finite timescales, we derive an exact expression for the path probabilities of continuous-time Markov chains from the path summation solution to the master equation. We present a minimal model for a driven system in which relative energies of the initial and target states control the speed, and the nonequilibrium currents of a cycle control the dissipation. Although the hypothesis holds near equilibrium, we find that faster processes can dissipate less under far-from-equilibrium conditions because of strong currents. This model serves as a minimal prototype for designing kinetics to sculpt the nonequilibrium path space so that faster paths produce less dissipation.
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Affiliation(s)
- Rebecca A Bone
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Daniel J Sharpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, Cambridge, United Kingdom
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, Cambridge, United Kingdom
| | - Jason R Green
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts 02125, USA.,Department of Physics, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
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11
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Nakamuro T, Kamei K, Sun K, Bode JW, Harano K, Nakamura E. Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions. J Am Chem Soc 2022; 144:13612-13622. [PMID: 35857028 DOI: 10.1021/jacs.2c03949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca2+-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca2+ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.
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Affiliation(s)
- Takayuki Nakamuro
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Kamei
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keyi Sun
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich 8093, Switzerland
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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12
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Russo J, Romano F, Kroc L, Sciortino F, Rovigatti L, Šulc P. SAT-assembly: a new approach for designing self-assembling systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:354002. [PMID: 35148521 DOI: 10.1088/1361-648x/ac5479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as building blocks, where the different units bind at specific interaction sites (the patches), and we exploit the possibility of having mixtures with several components. The interaction rules between the patches is determined by transforming the combinatorial problem into a Boolean satisfiability problem (SAT) which searches for solutions where all bonds are formed in the target structure. Additional conditions, such as the non-satisfiability of competing structures (e.g. metastable states) can be imposed, allowing to effectively design the assembly path in order to avoid kinetic traps. We demonstrate this approach by designing and numerically simulating a cubic diamond structure from four particle species that assembles without competition from other polymorphs, including the hexagonal structure.
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Affiliation(s)
- John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
- European Centre for Living Technology (ECLT) Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Lukáš Kroc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, United States of America
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
- Institute for Complex Systems, Uos Sapienza, CNR, Rome 00185, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, United States of America
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13
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Fan H, Li K, Tu T, Zhu X, Zhang L, Liu M. ATP-Induced Emergent Circularly Polarized Luminescence and Encryption. Angew Chem Int Ed Engl 2022; 61:e202200727. [PMID: 35195948 DOI: 10.1002/anie.202200727] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Indexed: 02/06/2023]
Abstract
Biomimetic ATP-driven supramolecular assembly is important to understand various biological processes and dissipative systems. Here, we report an ATP-driven chiral assembly exhibiting circularly polarized luminescence (CPL) via the interaction of an achiral terpyridine-based ZnII complex with nucleotides. It was found that while the metal complexes could co-assemble with the nucleotides to form fluorescent assemblies, only a combination of furan-substituted terpyridine complex and ATP showed an intense CPL with a dissymmetry factor (glum ) as high as 0.20. This means that the complex could recognize ATP using CPL as a readout signal, thus providing an example of ATP encryption. Interestingly, when ATP was transferred into ADP or AMP under enzymatic hydrolysis, the CPL decreases or disappears. Addition of ATP generates CPL again, thus producing an ATP-induced CPL system. This work presents the first example of ATP-induced CPL and encryption.
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Affiliation(s)
- Huahua Fan
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Li
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Tu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Xuefeng Zhu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
| | - Li Zhang
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China
| | - Minghua Liu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Fan H, Li K, Tu T, Zhu X, Zhang L, Liu M. ATP‐Induced Emergent Circularly Polarized Luminescence and Encryption. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Huahua Fan
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2 Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Kun Li
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2 Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Tao Tu
- Department of Chemistry Fudan University 220 Handan Road Shanghai 200433 China
| | - Xuefeng Zhu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2 Beijing 100190 China
| | - Li Zhang
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2 Beijing 100190 China
| | - Minghua Liu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2 Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
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15
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Bupathy A, Frenkel D, Sastry S. Temperature protocols to guide selective self-assembly of competing structures. Proc Natl Acad Sci U S A 2022; 119:2119315119. [PMID: 35165184 PMCID: PMC8872760 DOI: 10.1073/pnas.2119315119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Multicomponent self-assembly mixtures offer the possibility of encoding multiple target structures with the same set of interacting components. Selective retrieval of one of the stored structures has been attempted by preparing an initial state that favors the assembly of the required target, through seeding, concentration patterning, or specific choices of interaction strengths. This may not be possible in an experiment where on-the-fly reconfiguration of the building blocks to switch functionality may be required. In this paper, we explore principles of inverse design of a multicomponent, self-assembly mixture capable of encoding two competing structures that can be selected through simple temperature protocols. We design the target structures to realize the generic situation in which one of the targets has the lower nucleation barrier, while the other is globally more stable. We observe that, to avoid the formation of spurious or chimeric aggregates, the number of neighboring component pairs that occur in both structures should be minimal. Our design also requires the inclusion of components that are part of only one of the target structures. We observe, however, that to maximize the selectivity of retrieval, the component library itself should be maximally shared by the two targets, within such a constraint. We demonstrate that temperature protocols can be designed that lead to the formation of either one of the target structures with high selectivity. We discuss the important role played by secondary aggregation products in improving selectivity, which we term "vestigial aggregates."
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Affiliation(s)
- Arunkumar Bupathy
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Daan Frenkel
- Centre for Computational Chemistry, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Srikanth Sastry
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India;
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16
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Abstract
Time efficiency of self-assembly is crucial for many biological processes. Moreover, with the advances of nanotechnology, time efficiency in artificial self-assembly becomes ever more important. While structural determinants and the final assembly yield are increasingly well understood, kinetic aspects concerning the time efficiency, however, remain much more elusive. In computer science, the concept of time complexity is used to characterize the efficiency of an algorithm and describes how the algorithm's runtime depends on the size of the input data. Here we characterize the time complexity of nonequilibrium self-assembly processes by exploring how the time required to realize a certain, substantial yield of a given target structure scales with its size. We identify distinct classes of assembly scenarios, i.e., "algorithms" to accomplish this task, and show that they exhibit drastically different degrees of complexity. Our analysis enables us to identify optimal control strategies for nonequilibrium self-assembly processes. Furthermore, we suggest an efficient irreversible scheme for the artificial self-assembly of nanostructures, which complements the state-of-the-art approach using reversible binding reactions and requires no fine-tuning of binding energies.
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17
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Hensley A, Jacobs WM, Rogers WB. Self-assembly of photonic crystals by controlling the nucleation and growth of DNA-coated colloids. Proc Natl Acad Sci U S A 2022; 119:e2114050118. [PMID: 34949716 PMCID: PMC8740761 DOI: 10.1073/pnas.2114050118] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2021] [Indexed: 12/04/2022] Open
Abstract
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but their applications have been limited by poor understanding and control over the crystallization dynamics. To address this challenge, we use microfluidics to quantify the kinetics of DNA-programmed self-assembly along the entire crystallization pathway, from thermally activated nucleation through reaction-limited and diffusion-limited phases of crystal growth. Our detailed measurements of the temperature and concentration dependence of the kinetics at all stages of crystallization provide a stringent test of classical theories of nucleation and growth. After accounting for the finite rolling and sliding rates of micrometer-sized DNA-coated colloids, we show that modified versions of these classical theories predict the absolute nucleation and growth rates with quantitative accuracy. We conclude by applying our model to design and demonstrate protocols for assembling large single crystals with pronounced structural coloration, an essential step in creating next-generation optical metamaterials from colloids.
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Affiliation(s)
- Alexander Hensley
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - W Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453;
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18
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Stahley JB, Zanjani MB. Multifarious colloidal structures: new insight into ternary and quadripartite ordered assemblies. NANOSCALE 2021; 13:16554-16563. [PMID: 34558597 DOI: 10.1039/d1nr05635b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-mediated assembly of colloidal particles can be utilized to produce a variety of structures which may have desirable phononic, photonic, or electronic transport properties. Recent developments in linker-mediated assembly processes allow for interactions to be coordinated between many different types of colloidal particles more easily and with fewer unique sequences than direct hybridization. However, the dynamics of colloidal self-assembly becomes increasingly more complex when coordinating interactions between three or more distinct interacting elements. In such cases particle pairs with similar binding energies are allowed to interact unpredictably, and enthalpically degenerate binding sites will be noticeably more present while numerous secondary phases may also result from the self-assembly process. Therefore, it is necessary to develop procedures for predicting feasible superstructure geometries for these systems before they can be implemented in material design. Here we investigate the formation of multifarious ordered structures through self-assembly of multiple types of spherically symmetrical colloidal particles with a variety of interaction matrices. We utilize Molecular Dynamics (MD) simulations to study the growth behavior of systems with different types of interacting elements and different particle sizes, and also predict the formation and stability of the target structures. We also study the phononic spectra of various ternary structures in order to identify the influence of key structural parameters on phonon bandgap frequencies and ranges. Our results provide direct guidelines for designing ternary and quadripartite multifarious colloidal structures, and motivate new directions for future experimental work to target formation of multi-component colloidal superstructures beyond the well-established binary symmetries studied in the past.
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Affiliation(s)
- James B Stahley
- Department of Mechanical and Manufacturing Engineering, Miami University, Oxford, OH, USA.
| | - Mehdi B Zanjani
- Department of Mechanical and Manufacturing Engineering, Miami University, Oxford, OH, USA.
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19
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Mahynski NA, Shen VK. Symmetry-derived structure directing agents for two-dimensional crystals of arbitrary colloids. SOFT MATTER 2021; 17:7853-7866. [PMID: 34382053 PMCID: PMC9793339 DOI: 10.1039/d1sm00875g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We derive properties of self-assembling rings which can template the organization of an arbitrary colloid into any periodic symmetry in two Euclidean dimensions. By viewing this as a tiling problem, we illustrate how the shape and chemical patterning of these rings are derivable, and are explicitly reflected by the symmetry group's orbifold symbol. We performed molecular dynamics simulations to observe their self-assembly and found 5 different characteristics which could be easily rationalized on the basis of this symbol. These include systems which undergo chiral phase separation, are addressably complex, exhibit self-limiting growth into clusters, form ordered "rods" in only one-dimension akin to a smectic phase, and those from symmetry groups which are pluripotent and allow one to select rings which exhibit different behaviors. We discuss how the curvature of the ring's edges plays an integral role in achieving correct self-assembly, and illustrate how to obtain these shapes. This provides a method for patterning colloidal systems at interfaces without explicitly programming this information onto the colloid itself.
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Affiliation(s)
- Nathan A Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA.
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20
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Barcelona-Cazanave L, Trejo-Carbajal N, Rodríguez-González RJ, Larios-López L, Felix-Serrano I, Mata-Padilla JM, Navarro-Rodríguez D. Synthesis and thermotropic liquid-crystalline properties of a hexyloxy-substituted pyridyl-ethynylene-azobenzene and its halogen-bonded complex with tetrafluoroiodophenyl decanoate. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2021.109739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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22
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Xiao J, He Q, Yang M, Li H, Qiu X, Wang B, Zhang B, Bu W. Hierarchical self-assembly of miktoarm star copolymers with pathway complexity. Polym Chem 2021. [DOI: 10.1039/d0py01170c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-assembly of amphiphilic miktoarm star copolymers shows hierarchical pathway complexity from molecular building blocks to miktoarm stars to micellar nano-objects to complex hierarchical assemblies.
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Affiliation(s)
- Jie Xiao
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Qun He
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Minjun Yang
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Haoquan Li
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Xiandeng Qiu
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
| | - Binghua Wang
- School of Materials Science and Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Bin Zhang
- School of Materials Science and Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Weifeng Bu
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province
- State Key Laboratory of Applied Organic Chemistry
- and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
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23
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Rogers WB. A mean-field model of linker-mediated colloidal interactions. J Chem Phys 2020; 153:124901. [DOI: 10.1063/5.0020578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- W. Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, 02453, USA
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24
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Young KG, Najafi B, Sant WM, Contera S, Louis AA, Doye JPK, Turberfield AJ, Bath J. Reconfigurable T‐junction DNA Origami. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006281] [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)
| | - Behnam Najafi
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - William M. Sant
- Department of Chemistry University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Sonia Contera
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - Ard A. Louis
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - Jonathan P. K. Doye
- Department of Chemistry University of Oxford South Parks Road Oxford OX1 3QZ UK
| | | | - Jonathan Bath
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
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25
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Young KG, Najafi B, Sant WM, Contera S, Louis AA, Doye JPK, Turberfield AJ, Bath J. Reconfigurable T-junction DNA Origami. Angew Chem Int Ed Engl 2020; 59:15942-15946. [PMID: 32524699 DOI: 10.1002/anie.202006281] [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: 04/30/2020] [Indexed: 01/24/2023]
Abstract
DNA self-assembly allows the construction of nanometre-scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single-stranded loops embedded in a double-stranded DNA template and is programmed by a set of double-stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T-junctions formed by hybridization of single-stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T-junction origami motifs and that assembly can be performed at room temperature.
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Affiliation(s)
- Katherine G Young
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Behnam Najafi
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - William M Sant
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Sonia Contera
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Ard A Louis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Jonathan P K Doye
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | | | - Jonathan Bath
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
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26
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Xia X, Hu H, Ciamarra MP, Ni R. Linker-mediated self-assembly of mobile DNA-coated colloids. SCIENCE ADVANCES 2020; 6:eaaz6921. [PMID: 32637586 PMCID: PMC7314559 DOI: 10.1126/sciadv.aaz6921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Developing construction methods of materials tailored for given applications with absolute control over building block placement poses an immense challenge. DNA-coated colloids offer the possibility of realising programmable self-assembly, which, in principle, can assemble almost any structure in equilibrium, but remains challenging experimentally. Here, we propose an innovative system of linker-mediated mobile DNA-coated colloids (mDNACCs), in which mDNACCs are bridged by the free DNA linkers in solution, whose two single-stranded DNA tails can bind with specific single-stranded DNA receptors of complementary sequence coated on colloids. We formulate a mean-field theory efficiently calculating the effective interaction between mDNACCs, where the entropy of DNA linkers plays a nontrivial role. Particularly, when the binding between free DNA linkers in solution and the corresponding receptors on mDNACCs is strong, the linker-mediated colloidal interaction is determined by the linker entropy depending on the linker concentration.
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Affiliation(s)
- Xiuyang Xia
- Chemical Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hao Hu
- Chemical Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
- School of Physics and Materials Science, Anhui University, Hefei 230601, People’s Republic of China
| | - Massimo Pica Ciamarra
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Ran Ni
- Chemical Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
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27
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Characterization of 3D DNA Assemblies Using Cryogenic Electron Microscopy. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-9107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Mahynski NA, Mao R, Pretti E, Shen VK, Mittal J. Grand canonical inverse design of multicomponent colloidal crystals. SOFT MATTER 2020; 16:3187-3194. [PMID: 32134420 DOI: 10.1039/c9sm02426c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inverse design methods are powerful computational approaches for creating colloidal systems which self-assemble into a target morphology by reverse engineering the Hamiltonian of the system. Despite this, these optimization procedures tend to yield Hamiltonians which are too complex to be experimentally realized. An alternative route to complex structures involves the use of several different components, however, conventional inverse design methods do not explicitly account for the possibility of phase separation into compositionally distinct structures. Here, we present an inverse design scheme for multicomponent colloidal systems by combining active learning with a method to directly compute their ground state phase diagrams. This explicitly accounts for phase separation and can locate stable regions of Hamiltonian parameter space which grid-based surveys are prone to miss. Using this we design low-density, binary structures with Lennard-Jones-like pairwise interactions that are simpler than in the single component case and potentially realizable in an experimental setting. This reinforces the concept that ground states of simple, multicomponent systems might be rich with previously unappreciated diversity, enabling the assembly of non-trivial structures with only few simple components instead of a single complex one.
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Affiliation(s)
- Nathan A Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA.
| | - Runfang Mao
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Dr., Bethlehem, Pennsylvania 18015-4791, USA
| | - Evan Pretti
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Dr., Bethlehem, Pennsylvania 18015-4791, USA
| | - Vincent K Shen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA.
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Dr., Bethlehem, Pennsylvania 18015-4791, USA
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29
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020; 59:8594-8600. [PMID: 32043698 DOI: 10.1002/anie.201915063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/13/2020] [Indexed: 01/13/2023]
Abstract
Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a "seed" strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4-7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100082, China
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jie Song
- Department of Instrument Science and Engineering, School of Electronic Information and electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA, 30322, USA
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30
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Serizawa T, Maeda T, Sawada T. Neutralization-Induced Self-Assembly of Cellulose Oligomers into Antibiofouling Crystalline Nanoribbon Networks in Complex Mixtures. ACS Macro Lett 2020; 9:301-305. [PMID: 35648536 DOI: 10.1021/acsmacrolett.9b01008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular self-assembly in solutions is a powerful strategy for fabricating functional architectures. Various bio(macro)molecules have been used as self-assembly components. However, structural polysaccharides, such as cellulose and chitin, have rarely been a research focus for molecular self-assembly, even though their crystalline assemblies potentially have robust physicochemical properties. Herein, we demonstrated the neutralization-induced self-assembly of cellulose oligomers into antibiofouling crystalline nanoribbon networks to produce physically cross-linked hydrogels. The self-assembly proceeded even in versatile complex mixtures, such as serum-containing cell culture media, in a controlled manner for 3D cell culture. The cultured cells grew into cell aggregates (spheroids), which were simply collected through natural filtration due to the mechanically crushable property of the crystalline nanoribbons through water flow by pipetting. We will show the potential of cellulose oligomers for biocompatible, crystalline soft materials.
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Affiliation(s)
- Takeshi Serizawa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tohru Maeda
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Toshiki Sawada
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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31
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering College of Materials Science and Engineering Beijing University of Chemical Technology Beijing 100082 China
| | - Aleks Reinhardt
- Department of Chemistry University of Cambridge Cambridge CB2 1EW UK
| | - Pengfei Wang
- Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Jie Song
- Department of Instrument Science and Engineering School of Electronic Information and electrical Engineering Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Emory University School of Medicine Atlanta GA 30322 USA
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32
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Anamimoghadam O, Cooper JA, Nguyen MT, Guo Q, Mosca L, Roy I, Sun J, Stern CL, Redfern L, Farha OK, Stoddart JF. Cyclotris(paraquat‐
p
‐phenylenes). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ommid Anamimoghadam
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - James A. Cooper
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Minh T. Nguyen
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Qing‐Hui Guo
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Lorenzo Mosca
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Indranil Roy
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Junling Sun
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Charlotte L. Stern
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Louis Redfern
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Omar K. Farha
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - J. Fraser Stoddart
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
- Institute for Molecular Design and Synthesis Tianjin University 92 Weijin Road Tianjin 300072 China
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
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33
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Anamimoghadam O, Cooper JA, Nguyen MT, Guo Q, Mosca L, Roy I, Sun J, Stern CL, Redfern L, Farha OK, Stoddart JF. Cyclotris(paraquat‐
p
‐phenylenes). Angew Chem Int Ed Engl 2019; 58:13778-13783. [DOI: 10.1002/anie.201907329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/18/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Ommid Anamimoghadam
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - James A. Cooper
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Minh T. Nguyen
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Qing‐Hui Guo
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Lorenzo Mosca
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Indranil Roy
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Junling Sun
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Charlotte L. Stern
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Louis Redfern
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Omar K. Farha
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - J. Fraser Stoddart
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
- Institute for Molecular Design and Synthesis Tianjin University 92 Weijin Road Tianjin 300072 China
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
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34
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Lin G, Rahim MA, Leeming MG, Cortez-Jugo C, Besford QA, Ju Y, Zhong QZ, Johnston ST, Zhou J, Caruso F. Selective Metal-Phenolic Assembly from Complex Multicomponent Mixtures. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17714-17721. [PMID: 31038907 DOI: 10.1021/acsami.9b04195] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Selective self-assembly in multicomponent mixtures offers a method for isolating desired components from complex systems for the rapid production of functional materials. Developing approaches capable of selective assembly of "target" components into intended three-dimensional structures is challenging because of the intrinsically high complexity of multicomponent systems. Herein, we report the selective coordination-driven self-assembly of metal-phenolic networks (MPNs) from a series of complex multicomponent systems (including crude plant extracts) into thin films via metal chelation with phenolic ligands. The metal (FeIII) selectively assembles low abundant phenolic components (e.g., myricetrin and quercetrin) from plant extracts into thin films. This selective metal-phenolic assembly is independent of the substrate properties (e.g., size, surface charge, and shape). Moreover, the high selectivity is consistent across different target phenolic ligands in model mixtures, even though each individual component can form thin films from single-component systems. A computational simulation of film formation suggests that the driving force for the selective behavior stems from differences in the number of chelating sites in the phenolic structures. The MPN films are shown to demonstrate improved antioxidant properties compared with the corresponding phenolic compounds in their free form, therefore exhibiting potential as free-standing antioxidant films.
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35
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Hou G, Xia X, Liu J, Wang W, Dong M, Zhang L. Designing Superlattice Structure via Self-Assembly of One-Component Polymer-Grafted Nanoparticles. J Phys Chem B 2019; 123:2157-2168. [PMID: 30742436 DOI: 10.1021/acs.jpcb.8b11118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The control of the self-assembly of the nanocrystals into ordered structures has been extensively investigated, but fewer efforts have been devoted to studying one-component polymer-grafted nanoparticles (OPNPs). Herein, through coarse-grained molecular dynamics simulation, we design a novel nanoparticle (NP) grafted with polymer chains, focusing on its self-assembled structures. First, we examine the effects of length and density of grafted polymer chains by calculating the radial distribution function between NPs, as well as through direct visualization. We observe a monotonic change of the arranged morphology of grafted-NPs as a function of the density of grafted polymer chains, which indicates that the increase of the grafting density contributes to the order of the morphology. Meanwhile, we find that much longer grafted polymer chains worsen the regularity of the morphology. Then, we probe the influence of the stiffness of grafted polymer chains (denoted by K ranging from 0 to 500) on the order of grafted-NPs, finding that the order of the structure exhibits a nonmonotonic behavior as a function of K at moderate grafting density. For high grafting density, the order of the morphology is initially enhanced and becomes saturated as a function of K. For the effect of K on the stress-strain behavior, the system with the lowest order demonstrates the most remarkable reinforced mechanical behavior for both low and high grafting density. Last, we establish the phase diagram by varying the stiffness and density of the grafted polymer chains, which contains the amorphous, ordered, and superlattice structures, respectively. In general, our simulated results provide guidelines to tailor the self-assembly of the OPNPs by taking advantage of the length, density, and stiffness of grafted polymer chains.
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Affiliation(s)
| | - Xiuyang Xia
- Chemical Engineering, School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , 637459 , Singapore
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36
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Gorla L, Martí-Centelles V, Altava B, Burguete MI, Luis SV. The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives. CrystEngComm 2019. [DOI: 10.1039/c8ce02088d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Side chain as the main conformational and self-assembly structural factor for C2-pseudopeptides.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | | | - Belén Altava
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
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37
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Adamantane template effect on the self-assembly of a molecular tetrahedron: A theoretical analysis. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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38
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Adorf CS, Antonaglia J, Dshemuchadse J, Glotzer SC. Inverse design of simple pair potentials for the self-assembly of complex structures. J Chem Phys 2018; 149:204102. [DOI: 10.1063/1.5063802] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Carl S. Adorf
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - James Antonaglia
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Julia Dshemuchadse
- Department of Chemical Engineering, 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
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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39
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Madge J, Bourne D, Miller MA. Controlling Fragment Competition on Pathways to Addressable Self-Assembly. J Phys Chem B 2018; 122:9815-9825. [PMID: 30256103 DOI: 10.1021/acs.jpcb.8b08096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building blocks, each of which occupies a defined location in the target. The requirement that each type of building block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap, since they cannot be combined. Here, we introduce a "completability" algorithm to quantify competition between self-assembling fragments and use it to deduce general principles for suppressing the effects of fragment incompatibility in the self-assembly of small addressable clusters. Competition originates from loops in the bonding network of the target structure, but loops may be needed to provide structural rigidity and thermodynamic stability. An optimal compromise can be achieved by careful choice of bonding networks and by promoting semihierarchical pathways that rule out competition between early fragments. These concepts are illustrated in simulations of self-assembly in two contrasting addressable targets of 20 unique components each.
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40
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Niebuur BJ, Chiappisi L, Zhang X, Jung F, Schulte A, Papadakis CM. Formation and Growth of Mesoglobules in Aqueous Poly( N-isopropylacrylamide) Solutions Revealed with Kinetic Small-Angle Neutron Scattering and Fast Pressure Jumps. ACS Macro Lett 2018; 7:1155-1160. [PMID: 35651267 DOI: 10.1021/acsmacrolett.8b00605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The phase transition from swollen chains to polymer mesoglobules of an aqueous solution of poly(N-isopropylacrylamide) is investigated with kinetic small-angle neutron scattering with 50 ms time resolution in conjunction with millisecond pressure jumps across the coexistence line. The time-resolved study evidenced three distinct regimes: fractal clusters form during the first second and transform into compact mesoglobules. During the following ∼20 s, these grow by diffusion-limited coalescence. The final step consists of a slow growth characterized by an energy barrier of several kBT. The method opens opportunities for kinetic structural studies of multicomponent systems over wide length and time scales and gives a structural picture spanning from the chain collapse to mesoscopic phase separation.
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Affiliation(s)
- Bart-Jan Niebuur
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Leonardo Chiappisi
- Institut Laue-Langevin, Large Scale Structures Group, 6, rue Jules Horowitz, 38042 Grenoble, France
- Technische Universität Berlin, Stranski Laboratorium für Physikalische Chemie und Theoretische Chemie, Institut für Chemie, Straße des 17. Juni 124, Sekr. TC7, D-10623 Berlin, Germany
| | - Xiaohan Zhang
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Florian Jung
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
| | - Alfons Schulte
- Department of Physics and College of Optics and Photonics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816-2385, United States
| | - Christine M. Papadakis
- Technische Universität München, Physik-Department, Fachgebiet Physik weicher Materie, James-Franck-Str. 1, 85748 Garching, Germany
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41
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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42
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Fonseca P, Romano F, Schreck JS, Ouldridge TE, Doye JPK, Louis AA. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J Chem Phys 2018; 148:134910. [PMID: 29626893 DOI: 10.1063/1.5019344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
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Affiliation(s)
- Pedro Fonseca
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, USA
| | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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43
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Bouju X, Duguet É, Gauffre F, Henry CR, Kahn ML, Mélinon P, Ravaine S. Nonisotropic Self-Assembly of Nanoparticles: From Compact Packing to Functional Aggregates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706558. [PMID: 29740924 DOI: 10.1002/adma.201706558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/07/2017] [Indexed: 06/08/2023]
Abstract
Quantum strongly correlated systems that exhibit interesting features in condensed matter physics often need an unachievable temperature or pressure range in classical materials. One solution is to introduce a scaling factor, namely, the lattice parameter. Synthetic heterostructures named superlattices or supracrystals are synthesized by the assembling of colloidal atoms. These include semiconductors, metals, and insulators for the exploitation of their unique properties. Most of them are currently limited to dense packing. However, some of desired properties need to adjust the colloidal atoms neighboring number. Here, the current state of research in nondense packing is summarized, discussing the benefits, outlining possible scenarios and methodologies, describing examples reported in the literature, briefly discussing the challenges, and offering preliminary conclusions. Penetrating such new and intriguing research fields demands a multidisciplinary approach accounting for the coupling of statistic physics, solid state and quantum physics, chemistry, computational science, and mathematics. Standard interactions between colloidal atoms and emerging fields, such as the use of Casimir forces, are reported. In particular, the focus is on the novelty of patchy colloidal atoms to meet this challenge.
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Affiliation(s)
- Xavier Bouju
- Centre d'élaboration de matériaux et d'études structurales (CEMES), CNRS, Université de Toulouse, UPR CNRS 8011, 29 Rue J. Marvig, F-31055, Toulouse, France
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
| | - Étienne Duguet
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
- CNRS, Univ. Bordeaux, ICMCB, UMR 5026, F-33600, Pessac, France
| | - Fabienne Gauffre
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
- Institut des sciences chimiques de Rennes (ISCR), CNRS, Université de Rennes, UMR CNRS 6226, 263 avenue du Général Leclerc, F-35000, Rennes, France
| | - Claude R Henry
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
- Centre interdisciplinaire de nanoscience de Marseille (CINAM), CNRS, Aix-Marseille Université, UMR CNRS 7325, Campus de Luminy, F-13288, Marseille, France
| | - Myrtil L Kahn
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
- Laboratoire de chimie de coordination (LCC), CNRS, Université de Toulouse, UPR CNRS 8241, F-31000, Toulouse, France
| | - Patrice Mélinon
- Observatoire des micro et nanotechnologies (OMNT), Minatec, 17 rue des Martyrs, F-38000, Grenoble, France
- Institut Lumière Matière (ILM), CNRS, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5306, F-69622, Villeurbanne, France
| | - Serge Ravaine
- CNRS, Univ. Bordeaux, CRPP, UMR 5031, F-33600, Pessac, France
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Direct observation and rational design of nucleation behavior in addressable self-assembly. Proc Natl Acad Sci U S A 2018; 115:E5877-E5886. [PMID: 29891671 PMCID: PMC6042111 DOI: 10.1073/pnas.1806010115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems. To optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on a prototypical “DNA-brick” structure. By combining temperature-dependent dynamic light scattering and atomic force microscopy with coarse-grained simulations, we show how subtle changes in the nucleation pathway profoundly affect the yield of the correctly formed structures. In particular, we can increase the range of conditions over which self-assembly occurs by using stable multisubunit clusters that lower the nucleation barrier for assembling subunits in the interior of the structure. Consequently, modifying only a small portion of a structure is sufficient to optimize its assembly. Due to the generality of our coarse-grained model and the excellent agreement that we find with our experimental results, the design principles reported here are likely to apply generically to addressable, multicomponent self-assembly.
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45
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Düring J, Haschke S, Bachmann J, Gröhn F. Porphyrin microneedles—structure control and catalytic activity. Colloid Polym Sci 2018. [DOI: 10.1007/s00396-018-4333-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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46
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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47
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Araújo NAM, da Costa RA, Dorogovtsev SN, Mendes JFF. Finding the Optimal Nets for Self-Folding Kirigami. PHYSICAL REVIEW LETTERS 2018; 120:188001. [PMID: 29775357 DOI: 10.1103/physrevlett.120.188001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Three-dimensional shells can be synthesized from the spontaneous self-folding of two-dimensional templates of interconnected panels, called nets. However, some nets are more likely to self-fold into the desired shell under random movements. The optimal nets are the ones that maximize the number of vertex connections, i.e., vertices that have only two of its faces cut away from each other in the net. Previous methods for finding such nets are based on random search, and thus, they do not guarantee the optimal solution. Here, we propose a deterministic procedure. We map the connectivity of the shell into a shell graph, where the nodes and links of the graph represent the vertices and edges of the shell, respectively. Identifying the nets that maximize the number of vertex connections corresponds to finding the set of maximum leaf spanning trees of the shell graph. This method allows us not only to design the self-assembly of much larger shell structures but also to apply additional design criteria, as a complete catalog of the maximum leaf spanning trees is obtained.
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Affiliation(s)
- N A M Araújo
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Centro de Física Teórica e Computacional, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - R A da Costa
- Department of Physics and I3N, University of Aveiro, 3810-193 Aveiro, Portugal
| | - S N Dorogovtsev
- Department of Physics and I3N, University of Aveiro, 3810-193 Aveiro, Portugal
- A. F. Ioffe Physico-Technical Institute, 194021 St. Petersburg, Russia
| | - J F F Mendes
- Department of Physics and I3N, University of Aveiro, 3810-193 Aveiro, Portugal
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48
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Mishra A, Korlepara DB, Kumar M, Jain A, Jonnalagadda N, Bejagam KK, Balasubramanian S, George SJ. Biomimetic temporal self-assembly via fuel-driven controlled supramolecular polymerization. Nat Commun 2018; 9:1295. [PMID: 29602946 PMCID: PMC5878180 DOI: 10.1038/s41467-018-03542-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/22/2018] [Indexed: 12/26/2022] Open
Abstract
Temporal control of supramolecular assemblies to modulate the structural and transient characteristics of synthetic nanostructures is an active field of research within supramolecular chemistry. Molecular designs to attain temporal control have often taken inspiration from biological assemblies. One such assembly in Nature which has been studied extensively, for its well-defined structure and programmable self-assembly, is the ATP-driven seeded self-assembly of actin. Here we show, in a synthetic manifestation of actin self-assembly, an ATP-selective and ATP-fuelled, controlled supramolecular polymerization of a phosphate receptor functionalised monomer. It undergoes fuel-driven nucleation and seeded growth that provide length control and narrow dispersity of the resultant assemblies. Furthermore, coupling via ATP-hydrolysing enzymes yielded its transient characteristics. These results will usher investigations into synthetic analogues of important biological self-assembly motifs and will prove to be a significant advancement toward biomimetic temporally programmed materials.
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Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Divya B Korlepara
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Mohit Kumar
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Ankit Jain
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Narendra Jonnalagadda
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Karteek K Bejagam
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Sundaram Balasubramanian
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
| | - Subi J George
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
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49
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Fejer SN, Mantell RG, Wales DJ. Designing hierarchical molecular complexity: icosahedra of addressable icosahedra. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1439190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | | | - David J. Wales
- University Chemical Laboratories, University of Cambridge , Cambridge, UK
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50
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Madge J, Miller MA. Optimising minimal building blocks for addressable self-assembly. SOFT MATTER 2017; 13:7780-7792. [PMID: 29018850 DOI: 10.1039/c7sm01646h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Addressable structures are characterised by the set of unique components from which they are built and by the specific location that each component occupies. For an addressable structure to self-assemble, its constituent building blocks must be encoded with sufficient information to define their positions with respect to each other and to enable them to navigate to those positions. DNA, with its vast scope for encoding specific interactions, has been successfully used to synthesise addressable systems of several hundred components. In this work we examine the complementary question of the minimal requirements for building blocks to undergo addressable self-assembly driven by a controlled temperature quench. Our testbed is an idealised model of cubic particles patterned with attractive interactions. We introduce a scheme for optimising the interactions using a variant of basin-hopping and a negative design principle. The designed building blocks are tested dynamically in simple target structures to establish how their complexity affects the limits of reliable self-assembly.
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Affiliation(s)
- Jim Madge
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK.
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