1
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Nag S, Bisker G. Driven Self-Assembly of Patchy Particles Overcoming Equilibrium Limitations. J Chem Theory Comput 2024. [PMID: 39255461 PMCID: PMC11428128 DOI: 10.1021/acs.jctc.4c01118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Bridging biological complexity and synthetic material design, we investigate dissipative self-assembly in patchy particle systems. Utilizing Monte Carlo and Molecular Dynamics simulations, we demonstrate how external driving forces mitigate equilibrium trade-offs between assembly time and structural stability, traditionally encountered in self-assembly processes. Our findings also extend to biological-mimicking environments, where we explore the dynamics of patchy particles under crowded conditions. This comprehensive analysis offers insights into advanced material design, opening avenues for innovations in nanotechnology applications.
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Affiliation(s)
- Shubhadeep Nag
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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2
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Qi S, He X. Biomimetic Capsid-Like Nanoshells Self-Assembled from Homopolypeptides. Chemistry 2024; 30:e202401990. [PMID: 38923670 DOI: 10.1002/chem.202401990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
The preparation of capsid-like nanoshells and the elucidation of their formation pathways are crucial for the application potential of capsid-like nanomaterials. In this study, we have prepared biomimetic capsid-like nanoshells (CLNs) through the solution self-assembly of poly (β-phenethyl-L-aspartate) homopolypeptide (PPLA). The formation of CLNs is governed by an aggregation-fusion mechanism. Initially, PPLA molecules self-assemble into small spherical assemblies as subunits and the initial nuclei are formed through fusing some subunits. Subsequently, additional subunits rapidly fuse onto these nuclei, leading to the growth of full or partial CLNs during the growth phase. Moreover, the suitable condition benefiting CLNs formation is clarified by a morphological phase diagram based on the initial PPLA concentration against water content. Molecular-level measurements suggest that the molecular flexibility of PPLA is a key factor in the arrangement and fusion of subunits for the formation of CLNs. These findings offer new perspectives for a deeper understanding of the formation pathways of capsid-like nanoshells derived from synthetic polymers.
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Affiliation(s)
- Shuo Qi
- School of Chemistry and Molecular Engineering, East China Normal University, No.500 Dongchuan Road, Shanghai, 200241, China
| | - Xiaohua He
- School of Chemistry and Molecular Engineering, East China Normal University, No.500 Dongchuan Road, Shanghai, 200241, China
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3
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Niblo JK, Swartley JR, Zhang Z, DuBay KH. 2D capsid formation within an oscillatory energy landscape: orderly self-assembly depends on the interplay between a dynamic potential and intrinsic relaxation times. SOFT MATTER 2024; 20:6702-6713. [PMID: 39046256 DOI: 10.1039/d4sm00455h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Multiple dissipative self-assembly protocols designed to create novel structures or to reduce kinetic traps have recently emerged. Specifically, temporal oscillations of particle interactions have been shown effective at both aims, but investigations thus far have focused on systems of simple colloids or their binary mixtures. In this work, we expand our understanding of the effect of temporally oscillating interactions to a two-dimensional coarse-grained viral capsid-like model that undergoes a self-limited assembly. This model includes multiple intrinsic relaxation times due to the internal structure of the capsid subunits and, under certain interaction regimes, proceeds via a two-step nucleation mechanism. We find that oscillations much faster than the local intrinsic relaxation times can be described via a time averaged inter-particle potential across a wide range of interaction strengths, while oscillations much slower than these relaxation times result in structures that adapt to the attraction strength of the current half-cycle. Interestingly, oscillation periods similar to these relaxation times shift the interaction window over which orderly assembly occurs by enabling error correction during the half-cycles with weaker attractions. Our results provide fundamental insights to non-equilibrium self-assembly on temporally variant energy landscapes.
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Affiliation(s)
- Jessica K Niblo
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Jacob R Swartley
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
| | - Zhongmin Zhang
- Department of Chemistry, University of North Carolina at Chapel Hill, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Kateri H DuBay
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, VA 22903-4319, USA.
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4
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Navas SF, Klapp SHL. Impact of non-reciprocal interactions on colloidal self-assembly with tunable anisotropy. J Chem Phys 2024; 161:054908. [PMID: 39105552 DOI: 10.1063/5.0214730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024] Open
Abstract
Non-reciprocal (NR) effective interactions violating Newton's third law occur in many biological systems, but can also be engineered in synthetic, colloidal systems. Recent research has shown that such NR interactions can have tremendous effects on the overall collective behavior and pattern formation, but can also influence aggregation processes on the particle scale. Here, we focus on the impact of non-reciprocity on the self-assembly of a colloidal system (originally passive) with anisotropic interactions whose character is tunable by external fields. In the absence of non-reciprocity, that is, under equilibrium conditions, the colloids form square-like and hexagonal aggregates with extremely long lifetimes yet no large-scale phase separation [Kogler et al., Soft Matter 11, 7356 (2015)], indicating kinetic trapping. Here, we study, based on Brownian dynamics simulations in 2D, an NR version of this model consisting of two species with reciprocal isotropic, but NR anisotropic interactions. We find that NR induces an effective propulsion of particle pairs and small aggregates ("active colloidal molecules") forming at the initial stages of self-assembly, an indication of the NR-induced non-equilibrium. The shape and stability of these initial clusters strongly depend on the degree of anisotropy. At longer times, we find, for weak NR interactions, large (even system-spanning) clusters where single particles can escape and enter at the boundaries, in stark contrast to the small rigid aggregates appearing at the same time in the passive case. In this sense, weak NR shortcuts the aggregation. Increasing the degree of NR (and thus, propulsion), we even observe large-scale phase separation if the interactions are weakly anisotropic. In contrast, systems with strong NR and anisotropy remain essentially disordered. Overall, the NR interactions are shown to destabilize the rigid aggregates interrupting self-assembly and phase separation in the passive case, thereby helping the system to overcome kinetic barriers.
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Affiliation(s)
- Salman Fariz Navas
- Institute for Theoretical Physics, Technical University of Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Sabine H L Klapp
- Institute for Theoretical Physics, Technical University of Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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5
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Osat S, Metson J, Kardar M, Golestanian R. Escaping Kinetic Traps Using Nonreciprocal Interactions. PHYSICAL REVIEW LETTERS 2024; 133:028301. [PMID: 39073937 DOI: 10.1103/physrevlett.133.028301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 06/10/2024] [Indexed: 07/31/2024]
Abstract
Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a mechanism to escape kinetic traps by utilizing nonreciprocal interactions between components. Introducing nonequilibrium effects offered by broken action-reaction symmetry in the system pushes the trajectory of the system out of arrested dynamics. The dynamics of the model is studied using tools from the physics of interfaces and defects. Our proposal can find applications in self-assembly, glassy systems, and systems with arrested dynamics to facilitate escape from local minima in rough energy landscapes.
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6
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Batton CH, Rotskoff GM. Microscopic origin of tunable assembly forces in chiral active environments. SOFT MATTER 2024; 20:4111-4126. [PMID: 38726733 DOI: 10.1039/d4sm00247d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Across a variety of spatial scales, from nanoscale biological systems to micron-scale colloidal systems, equilibrium self-assembly is entirely dictated by-and therefore limited by-the thermodynamic properties of the constituent materials. In contrast, nonequilibrium materials, such as self-propelled active matter, expand the possibilities for driving the assemblies that are inaccessible in equilibrium conditions. Recently, a number of works have suggested that active matter drives or accelerates self-organization, but the emergent interactions that arise between solutes immersed in actively driven environments are complex and poorly understood. Here, we analyze and resolve two crucial questions concerning actively driven self-assembly: (i) how, mechanistically, do active environments drive self-assembly of passive solutes? (ii) Under which conditions is this assembly robust? We employ the framework of odd hydrodynamics to theoretically explain numerical and experimental observations that chiral active matter, i.e., particles driven with a directional torque, produces robust and long-ranged assembly forces. Together, these developments constitute an important step towards a comprehensive theoretical framework for controlling self-assembly in nonequilibrium environments.
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Affiliation(s)
- Clay H Batton
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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7
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Jhaveri A, Loggia S, Qian Y, Johnson ME. Discovering optimal kinetic pathways for self-assembly using automatic differentiation. Proc Natl Acad Sci U S A 2024; 121:e2403384121. [PMID: 38691585 PMCID: PMC11087789 DOI: 10.1073/pnas.2403384121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024] Open
Abstract
Macromolecular complexes are often composed of diverse subunits. The self-assembly of these subunits is inherently nonequilibrium and must avoid kinetic traps to achieve high yield over feasible timescales. We show how the kinetics of self-assembly benefits from diversity in subunits because it generates an expansive parameter space that naturally improves the "expressivity" of self-assembly, much like a deeper neural network. By using automatic differentiation algorithms commonly used in deep learning, we searched the parameter spaces of mass-action kinetic models to identify classes of kinetic protocols that mimic biological solutions for productive self-assembly. Our results reveal how high-yield complexes that easily become kinetically trapped in incomplete intermediates can instead be steered by internal design of rate-constants or external and active control of subunits to efficiently assemble. Internal design of a hierarchy of subunit binding rates generates self-assembly that can robustly avoid kinetic traps for all concentrations and energetics, but it places strict constraints on selection of relative rates. External control via subunit titration is more versatile, avoiding kinetic traps for any system without requiring molecular engineering of binding rates, albeit less efficiently and robustly. We derive theoretical expressions for the timescales of kinetic traps, and we demonstrate our optimization method applies not just for design but inference, extracting intersubunit binding rates from observations of yield-vs.-time for a heterotetramer. Overall, we identify optimal kinetic protocols for self-assembly as a powerful mechanism to achieve efficient and high-yield assembly in synthetic systems whether robustness or ease of "designability" is preferred.
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Affiliation(s)
- Adip Jhaveri
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Spencer Loggia
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Yian Qian
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Margaret E. Johnson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
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8
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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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9
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Rinkovec T, Kalebic D, Dehaen W, Whitelam S, Harvey JN, De Feyter S. On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface. Chem Sci 2024; 15:6076-6087. [PMID: 38665531 PMCID: PMC11041291 DOI: 10.1039/d4sc00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.
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Affiliation(s)
- Tamara Rinkovec
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Demian Kalebic
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Wim Dehaen
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Steven De Feyter
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
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10
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Pinto DEP, Araújo NAM, Šulc P, Russo J. Inverse Design of Self-Folding 3D Shells. PHYSICAL REVIEW LETTERS 2024; 132:118201. [PMID: 38563942 DOI: 10.1103/physrevlett.132.118201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Self-folding is an emerging paradigm for the inverse design of three-dimensional structures. While most efforts have concentrated on the shape of the net, our approach introduces a new design dimension-bond specificity between the edges. We transform this design process into a Boolean satisfiability problem to derive solutions for various target structures. This method significantly enhances the yield of the folding process. Furthermore, by linearly combining independent solutions, we achieve designs for shape-shifting nets wherein the dominant structure evolves with varying external conditions. This approach is demonstrated through coarse-grained simulations on two examples of triangular and square nets capable of folding into multiple target shapes.
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Affiliation(s)
- Diogo E P Pinto
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nuno A M Araújo
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
- TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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11
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Li M, Liu M, Qi F, Lin FR, Jen AKY. Self-Assembled Monolayers for Interfacial Engineering in Solution-Processed Thin-Film Electronic Devices: Design, Fabrication, and Applications. Chem Rev 2024; 124:2138-2204. [PMID: 38421811 DOI: 10.1021/acs.chemrev.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Interfacial engineering has long been a vital means of improving thin-film device performance, especially for organic electronics, perovskites, and hybrid devices. It greatly facilitates the fabrication and performance of solution-processed thin-film devices, including organic field effect transistors (OFETs), organic solar cells (OSCs), perovskite solar cells (PVSCs), and organic light-emitting diodes (OLEDs). However, due to the limitation of traditional interfacial materials, further progress of these thin-film devices is hampered particularly in terms of stability, flexibility, and sensitivity. The deadlock has gradually been broken through the development of self-assembled monolayers (SAMs), which possess distinct benefits in transparency, diversity, stability, sensitivity, selectivity, and surface passivation ability. In this review, we first showed the evolution of SAMs, elucidating their working mechanisms and structure-property relationships by assessing a wide range of SAM materials reported to date. A comprehensive comparison of various SAM growth, fabrication, and characterization methods was presented to help readers interested in applying SAM to their works. Moreover, the recent progress of the SAM design and applications in mainstream thin-film electronic devices, including OFETs, OSCs, PVSCs and OLEDs, was summarized. Finally, an outlook and prospects section summarizes the major challenges for the further development of SAMs used in thin-film devices.
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Affiliation(s)
- Mingliang Li
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Ming Liu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Feng Qi
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Francis R Lin
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Alex K-Y Jen
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Hong Kong Institute for Clean Energy, City University of Hong Kong, Kowloon, Hong Kong 999077, China
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 999077, China
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12
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Chennakesavalu S, Manikandan SK, Hu F, Rotskoff GM. Adaptive nonequilibrium design of actin-based metamaterials: Fundamental and practical limits of control. Proc Natl Acad Sci U S A 2024; 121:e2310238121. [PMID: 38359294 PMCID: PMC10895351 DOI: 10.1073/pnas.2310238121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/13/2023] [Indexed: 02/17/2024] Open
Abstract
The adaptive and surprising emergent properties of biological materials self-assembled in far-from-equilibrium environments serve as an inspiration for efforts to design nanomaterials. In particular, controlling the conditions of self-assembly can modulate material properties, but there is no systematic understanding of either how to parameterize external control or how controllable a given material can be. Here, we demonstrate that branched actin networks can be encoded with metamaterial properties by dynamically controlling the applied force under which they grow and that the protocols can be selected using multi-task reinforcement learning. These actin networks have tunable responses over a large dynamic range depending on the chosen external protocol, providing a pathway to encoding "memory" within these structures. Interestingly, we obtain a bound that relates the dissipation rate and the rate of "encoding" that gives insight into the constraints on control-both physical and information theoretical. Taken together, these results emphasize the utility and necessity of nonequilibrium control for designing self-assembled nanostructures.
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Affiliation(s)
| | | | - Frank Hu
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Grant M. Rotskoff
- Department of Chemistry, Stanford University, Stanford, CA94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA94305
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13
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Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024; 128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.
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Affiliation(s)
- Luc F Christians
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ethan V Halingstad
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Emiel Kram
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Evan M Okolovitch
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative Biosciences and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
- Materials Science Program, Colorado School of Mines, Golden, Colorado 80401, United States
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14
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Caporusso CB, Negro G, Suma A, Digregorio P, Carenza LN, Gonnella G, Cugliandolo LF. Phase behaviour and dynamics of three-dimensional active dumbbell systems. SOFT MATTER 2024; 20:923-939. [PMID: 38189452 DOI: 10.1039/d3sm01030a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We present a comprehensive numerical study of the phase behavior and dynamics of a three-dimensional active dumbbell system with attractive interactions. We demonstrate that attraction is essential for the system to exhibit nontrivial phases. We construct a detailed phase diagram by exploring the effects of the system's activity, density, and attraction strength. We identify several distinct phases, including a disordered, a gel, and a completely phase-separated phase. Additionally, we discover a novel dynamical phase, that we name percolating network, which is characterized by the presence of a spanning network of connected dumbbells. In the phase-separated phase we characterize numerically and describe analytically the helical motion of the dense cluster.
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Affiliation(s)
- C B Caporusso
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - G Negro
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - A Suma
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - P Digregorio
- Departement de Fisica de la Materia Condensada, Facultat de Fisica, Universitat de Barcelona, Martí i Franquès 1, E08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
| | - L N Carenza
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
- Department of Physics, Koç University, Rumelifeneri Yolu, 34450 Saryer, Istanbul, Turkey
| | - G Gonnella
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - L F Cugliandolo
- CNRS, Laboratoire de Physique Théorique et Hautes Energies, LPTHE, Sorbonne Université, F-75005 Paris, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
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15
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Beneduce C, Sciortino F, Šulc P, Russo J. Engineering Azeotropy to Optimize the Self-Assembly of Colloidal Mixtures. ACS NANO 2023; 17:24841-24853. [PMID: 38048489 PMCID: PMC10753881 DOI: 10.1021/acsnano.3c05569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023]
Abstract
The goal of inverse self-assembly is to design interparticle interactions capable of assembling the units into a desired target structure. The effective assembly of complex structures often requires the use of multiple components, each new component increasing the thermodynamic degrees of freedom and, hence, the complexity of the self-assembly pathway. In this work we explore the possibility to use azeotropy, i.e., a special thermodynamic condition where the system behaves effectively as a one-component system, as a way to control the self-assembly of an arbitrary number of components. Exploiting the mass-balance equations, we show how to select patchy particle systems that exhibit azeotropic points along the desired self-assembly pathway. As an example we map the phase diagram of a binary mixture that, by design, fully assembles into cubic (and only cubic) diamond crystal via an azeotropic point. The ability to explicitly include azeotropic points in artificial designs reveals effective pathways for the self-assembly of complex structures.
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Affiliation(s)
- Camilla Beneduce
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sciortino
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Petr Šulc
- School
of Molecular Sciences and Center for Molecular Design and Biomimetics,
The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, United States
- School
of Natural Sciences, Department of Bioscience, TU Munich, Am Coulombwall
4a, 85748, Garching, Germany
| | - John Russo
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
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16
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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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17
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Hendley RS, Zhang L, Bevan MA. Multistate Dynamic Pathways for Anisotropic Colloidal Assembly and Reconfiguration. ACS NANO 2023; 17:20512-20524. [PMID: 37788439 DOI: 10.1021/acsnano.3c07202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
We report the controlled interfacial assembly and reconfiguration of rectangular prism colloidal particles between microstructures of varying positional and orientational order including stable, metastable, and transient states. Structurally diverse states are realized by programming time dependent electric fields that mediate dipolar interactions determining particle position, orientation, compression, and chaining. We identify an order parameter set that defines each state as a combination of the positional and orientational order. These metrics are employed as reaction coordinates to capture the microstructure evolution between initial and final states upon field changes. Assembly trajectory manifolds between states in the low-dimensional reaction coordinate space reveal a dynamic pathway map including information about pathway accessibility, reversibility, and kinetics. By navigating the dynamic pathway map, we demonstrate reconfiguration between states on minute time scales, which is practically useful for particle-based materials processing and device responses. Our findings demonstrate a conceptually general approach to discover dynamic pathways as a basis to control assembly and reconfiguration of self-organizing building blocks that respond to global external stimuli.
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Affiliation(s)
- Rachel S Hendley
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Lechuan Zhang
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael A Bevan
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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18
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Das A, Limmer DT. Nonequilibrium design strategies for functional colloidal assemblies. Proc Natl Acad Sci U S A 2023; 120:e2217242120. [PMID: 37748070 PMCID: PMC10556551 DOI: 10.1073/pnas.2217242120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 08/17/2023] [Indexed: 09/27/2023] Open
Abstract
We use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.
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Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, CA94720
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, CA94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Kavli Energy NanoSciences Institute, University of California, Berkeley, CA94720
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19
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Jhaveri A, Loggia S, Qian Y, Johnson ME. Discovering optimal kinetic pathways for self-assembly using automatic differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555551. [PMID: 37693527 PMCID: PMC10491160 DOI: 10.1101/2023.08.30.555551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
During self-assembly of macromolecules ranging from ribosomes to viral capsids, the formation of long-lived intermediates or kinetic traps can dramatically reduce yield of the functional products. Understanding biological mechanisms for avoiding traps and efficiently assembling is essential for designing synthetic assembly systems, but learning optimal solutions requires numerical searches in high-dimensional parameter spaces. Here, we exploit powerful automatic differentiation algorithms commonly employed by deep learning frameworks to optimize physical models of reversible self-assembly, discovering diverse solutions in the space of rate constants for 3-7 subunit complexes. We define two biologically-inspired protocols that prevent kinetic trapping through either internal design of subunit binding kinetics or external design of subunit titration in time. Our third protocol acts to recycle intermediates, mimicking energy-consuming enzymes. Preventative solutions via interface design are the most efficient and scale better with more subunits, but external control via titration or recycling are effective even for poorly evolved binding kinetics. Whilst all protocols can produce good solutions, diverse subunits always helps; these complexes access more efficient solutions when following external control protocols, and are simpler to design for internal control, as molecular interfaces do not need modification during assembly given sufficient variation in dimerization rates. Our results identify universal scaling in the cost of kinetic trapping, and provide multiple strategies for eliminating trapping and maximizing assembly yield across large parameter spaces.
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Affiliation(s)
| | | | - Yian Qian
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
| | - Margaret E. Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218
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20
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Hagan MF, Mohajerani F. Self-assembly coupled to liquid-liquid phase separation. PLoS Comput Biol 2023; 19:e1010652. [PMID: 37186597 PMCID: PMC10212142 DOI: 10.1371/journal.pcbi.1010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/25/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Affiliation(s)
- Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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21
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Lee JH, Jung Y. Anomalous Dynamical Phase Transitions of the Ising Model Studied by the Nonequilibrium Ensemble Method: Freezing-by-Heating and Permanent Liquid. J Phys Chem B 2023; 127:3939-3945. [PMID: 37079918 DOI: 10.1021/acs.jpcb.3c01625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
We investigate the nonequilibrium, dynamical phase transition behavior of the one-dimensional Ising model, using the trajectory ensemble approach in the context of the large deviation theory. We introduce a double-biased ensemble, named the s, g-ensemble, based on nonequilibrium steady-state trajectories. The ensemble invokes the time-integrated, trajectory energy as an order parameter, coupled to its conjugate g-field in addition to the dynamical activity and its conjugate field s in the trajectory space. Using the dynamical free energy obtained from the large deviation formalism, we explore the rich behaviors of the dynamical phase transition of the 1D Ising model in the (s, g, T) parameter space, with T being temperature. Among other features, we discover that novel, anomalous dynamical phase transitions are possible due to the decoupling between the dynamical activity and trajectory energy under specific conditions. In particular, we observe that the system exhibits a freezing-by-heating phenomenon as the dynamical activity decreases with temperature under a specific condition. We also find a permanent liquid phase when the equilibrium temperature and the nonequilibrium g-field are exactly balanced against each other. Our results provide a useful tool for exploring the dynamical phase transition phenomena to be investigated in various systems.
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Affiliation(s)
- Jay-Hak Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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22
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Pinto DEP, Šulc P, Sciortino F, Russo J. Design strategies for the self-assembly of polyhedral shells. Proc Natl Acad Sci U S A 2023; 120:e2219458120. [PMID: 37040398 PMCID: PMC10120017 DOI: 10.1073/pnas.2219458120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/16/2023] [Indexed: 04/12/2023] Open
Abstract
The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous aggregates. Here, we investigate in detail the problem of the self-assembly of the three Archimedean shells with five contact points per vertex, i.e., the icosahedron, the snub cube, and the snub dodecahedron. We use patchy particles with five interaction sites (or patches) as model for the building blocks and recast the assembly problem as a Boolean satisfiability problem (SAT) for the patch-patch interactions. This allows us to find effective designs for all targets and to selectively suppress unwanted structures. By tuning the geometrical arrangement and the specific interactions of the patches, we demonstrate that lowering the symmetry of the building blocks reduces the number of competing structures, which in turn can considerably increase the yield of the target structure. These results cement SAT-assembly as an invaluable tool to solve inverse design problems.
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Affiliation(s)
- Diogo E. P. Pinto
- Dipartimento di Fisica, Sapienza Università di Roma, Rome00185, Italy
| | - Petr Šulc
- Life and Medical Sciences (LIMES), University of Bonn, Bonn53121, Germany
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ85281
| | | | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, Rome00185, Italy
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23
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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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24
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Baule A, Sollich P. Exponential increase of transition rates in metastable systems driven by non-Gaussian noise. Sci Rep 2023; 13:3853. [PMID: 36890184 PMCID: PMC9995508 DOI: 10.1038/s41598-023-30577-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
Noise-induced escape from metastable states governs a plethora of transition phenomena in physics, chemistry, and biology. While the escape problem in the presence of thermal Gaussian noise has been well understood since the seminal works of Arrhenius and Kramers, many systems, in particular living ones, are effectively driven by non-Gaussian noise for which the conventional theory does not apply. Here we present a theoretical framework based on path integrals that allows the calculation of both escape rates and optimal escape paths for a generic class of non-Gaussian noises. We find that non-Gaussian noise always leads to more efficient escape and can enhance escape rates by many orders of magnitude compared with thermal noise, highlighting that away from equilibrium escape rates cannot be reliably modelled based on the traditional Arrhenius-Kramers result. Our analysis also identifies a new universality class of non-Gaussian noises, for which escape paths are dominated by large jumps.
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Affiliation(s)
- Adrian Baule
- School of Mathematical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-University Göttingen, 37077, Göttingen, Germany
- Department of Mathematics, King's College London, London, WC2R 2LS, UK
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25
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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26
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McDonald MN, Zhu Q, Paxton WF, Peterson CK, Tree DR. Active control of equilibrium, near-equilibrium, and far-from-equilibrium colloidal systems. SOFT MATTER 2023; 19:1675-1694. [PMID: 36790855 DOI: 10.1039/d2sm01447e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The development of top-down active control over bottom-up colloidal assembly processes has the potential to produce materials, surfaces, and objects with applications in a wide range of fields spanning from computing to materials science to biomedical engineering. In this review, we summarize recent progress in the field using a taxonomy based on how active control is used to guide assembly. We find there are three distinct scenarios: (1) navigating kinetic pathways to reach a desirable equilibrium state, (2) the creation of a desirable metastable, kinetically trapped, or kinetically arrested state, and (3) the creation of a desirable far-from-equilibrium state through continuous energy input. We review seminal works within this framework, provide a summary of important application areas, and present a brief introduction to the fundamental concepts of control theory that are necessary for the soft materials community to understand this literature. In addition, we outline current and potential future applications of actively-controlled colloidal systems, and we highlight important open questions and future directions.
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Affiliation(s)
- Mark N McDonald
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA.
| | - Qinyu Zhu
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA.
| | - Walter F Paxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Cameron K Peterson
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, Utah, USA
| | - Douglas R Tree
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA.
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27
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Cho W, Zhou Z, Lin R, Ondry JC, Talapin DV. Synthesis of Colloidal GaN and AlN Nanocrystals in Biphasic Molten Salt/Organic Solvent Mixtures under High-Pressure Ammonia. ACS NANO 2023; 17:1315-1326. [PMID: 36621974 DOI: 10.1021/acsnano.2c09552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Group III nitrides are of great technological importance for electronic devices. These materials have been widely manufactured via high-temperature methods such as physical vapor transport (PVT), chemical vapor deposition (CVD), and hydride vapor phase epitaxy (HVPE). The preparation of group III nitrides by colloidal synthesis methods would provide significant advantages in the form of optical tunability via size and shape control and enable cost reductions through scalable solution-based device integration. Solution syntheses of III-nitride nanocrystals, however, have been scarce, and the quality of the synthesized products has been unsatisfactory for practical use. Here, we report that incorporating a molten salt phase in solution synthesis can provide a viable option for producing crystalline III-nitride nanomaterials. Crystalline GaN and AlN nanomaterials can be grown in a biphasic molten-salt/organic-solvent mixture under an ammonia atmosphere at moderate temperatures (less than 300 °C) and stabilized under ambient conditions by postsynthetic treatment with organic surface ligands. We suggest that microscopic reversibility of monomer attachment, which is essential for crystalline growth, can be achieved in molten salt during the nucleation and the growth of the III-nitride nanocrystals. We also show that increased ammonia pressure increases the size of the GaN nanocrystals produced. This work demonstrates that use of molten salt and high-pressure reactants significantly expands the chemical scope of solution synthesis of inorganic nanomaterials.
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Affiliation(s)
- Wooje Cho
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Zirui Zhou
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Ruiming Lin
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Justin C Ondry
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60517, United States
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28
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Fussell SL, Royall CP, van Duijneveldt JS. Controlling Kinetic Pathways in Demixing Microgel-Micelle Mixtures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1010-1018. [PMID: 36621908 PMCID: PMC9878723 DOI: 10.1021/acs.langmuir.2c02583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/22/2022] [Indexed: 06/17/2023]
Abstract
We investigate the temperature-dependent phase behavior of mixtures of poly(N-isopropylacrylamide) (pNIPAM) microgel colloids and a triblock copolymer (PEO-PPO-PEO) surfactant. Usually, gelation in these systems results from an increase in temperature. Here we investigate the role of the heating rate, and surprisingly, we find that this causes the mechanism of aggregation to change from one which is driven by depletion of the microgels by the micelles at low temperatures to the association of the two species at high temperatures. We thus reveal two competing mechanisms for attractions between the microgel particles which can be controlled by changing the heating rate. We use this heating-rate-dependent response of the system to access multiple structures for the same system composition. Samples were found to demix into phases rich and poor in microgel particles at temperatures below 33 °C, under conditions where the microgels particles are partially swollen. Under rapid heating full demixing is bypassed, and gel networks are formed instead. The temperature history of the sample, therefore, allows for kinetic selection between different final structures, which may be metastable.
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Affiliation(s)
- S. L. Fussell
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Bristol
Centre for Functional Nanomaterials, University
of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
| | - C. P. Royall
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Bristol
Centre for Functional Nanomaterials, University
of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
- Gulliver
UMR CNRS 7083, ESPCI Paris, Université
PSL, 75005 Paris, France
- HH
Wills Physics Laboratory, University of
Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
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29
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Osat S, Golestanian R. Non-reciprocal multifarious self-organization. NATURE NANOTECHNOLOGY 2023; 18:79-85. [PMID: 36509920 PMCID: PMC9879770 DOI: 10.1038/s41565-022-01258-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/06/2022] [Indexed: 05/14/2023]
Abstract
A hallmark of living systems is the ability to employ a common set of building blocks that can self-organize into a multitude of different structures. This capability can only be afforded in non-equilibrium conditions, as evident from the energy-consuming nature of the plethora of such dynamical processes. To achieve automated dynamical control of such self-assembled structures and transitions between them, we need to identify the fundamental aspects of non-equilibrium dynamics that can enable such processes. Here we identify programmable non-reciprocal interactions as a tool to achieve such functionalities. The design rule is composed of reciprocal interactions that lead to the equilibrium assembly of the different structures, through a process denoted as multifarious self-assembly, and non-reciprocal interactions that give rise to non-equilibrium dynamical transitions between the structures. The design of such self-organized shape-shifting structures can be implemented at different scales, from nucleic acids and peptides to proteins and colloids.
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Affiliation(s)
- Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Göttingen, Germany.
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK.
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30
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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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31
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Bone RA, Green JR. Optimizing dynamical functions for speed with stochastic paths. J Chem Phys 2022; 157:224101. [PMID: 36546817 DOI: 10.1063/5.0125479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Living systems are built from microscopic components that function dynamically; they generate work with molecular motors, assemble and disassemble structures such as microtubules, keep time with circadian clocks, and catalyze the replication of DNA. How do we implement these functions in synthetic nanostructured materials to execute them before the onset of dissipative losses? Answering this question requires a quantitative understanding of when we can improve performance and speed while minimizing the dissipative losses associated with operating in a fluctuating environment. Here, we show that there are four modalities for optimizing dynamical functions that can guide the design of nanoscale systems. We analyze Markov models that span the design space: a clock, ratchet, replicator, and self-assembling system. Using stochastic thermodynamics and an exact expression for path probabilities, we classify these models of dynamical functions based on the correlation of speed with dissipation and with the chosen performance metric. We also analyze random networks to identify the model features that affect their classification and the optimization of their functionality. Overall, our results show that the possible nonequilibrium paths can determine our ability to optimize the performance of dynamical functions, despite ever-present dissipation, when there is a need for speed.
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Affiliation(s)
- Rebecca A Bone
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Jason R Green
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
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32
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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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33
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Geometrically programmed self-limited assembly of tubules using DNA origami colloids. Proc Natl Acad Sci U S A 2022; 119:e2207902119. [PMID: 36252043 PMCID: PMC9618141 DOI: 10.1073/pnas.2207902119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature is replete with self-assembled materials that have one or more self-limited dimensions, including shells, tubules, and fibers. Despite significant advances in making nanometer- and micrometer-scale subunits, the programmable assembly of similar self-limiting architectures from synthetic components has remained largely out of reach. In this article, we create geometrically programmed subunits using DNA origami and study their assembly into tubules with a self-limited width. We show that the average self-limited dimension can be tuned by changing the local curvature encoded in a single subunit. Exploiting the programmability of our system, we further test the tradeoffs between fidelity and complexity embodied by two paradigms for self-limited assembly: self-closure through programmed curvature and addressable assembly through programmed specific interactions. Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.
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34
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Fang H, Tyukodi B, Rogers WB, Hagan MF. Polymorphic self-assembly of helical tubules is kinetically controlled. SOFT MATTER 2022; 18:6716-6728. [PMID: 36039801 PMCID: PMC9472595 DOI: 10.1039/d2sm00679k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger than the size scale of the individual monomers. In many such cases, the finite dimension is selected by a preferred curvature of the monomers, which leads to self-closure of the assembly. In this article, we study an example class of self-closing assemblies: cylindrical tubules that assemble from triangular monomers. By combining kinetic Monte Carlo simulations, free energy calculations, and simple theoretical models, we show that a range of programmable size scales can be targeted by controlling the intricate balance between the preferred curvature of the monomers and their interaction strengths. However, their assembly is kinetically controlled-the tubule morphology is essentially fixed shortly after closure, resulting in a distribution of tubule widths that is significantly broader than the equilibrium distribution. We develop a simple kinetic model based on this observation and the underlying free-energy landscape of assembling tubules that quantitatively describes the distributions. Our results are consistent with recent experimental observations of tubule assembly from triangular DNA origami monomers. The modeling framework elucidates design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality.
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Affiliation(s)
- Huang Fang
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
- Department of Physics, Babes-Bolyai University, 400084 Cluj-Napoca, Romania
| | - W Benjamin Rogers
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
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35
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Li M, Li ZW, Lyu Q, Peng B, Zhong R, Zhao M, Xiong B, Yi GR, Zhang L, Zhu J. Structure-Tunable Construction of Colloidal Photonic Composites via Kinetically Controlled Supramolecular Crosslinking. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miaomiao Li
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhan-Wei Li
- State Key Lab of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Quanqian Lyu
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Bolun Peng
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Rui Zhong
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Meiru Zhao
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Bijin Xiong
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Gi-Ra Yi
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Lianbin Zhang
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Jintao Zhu
- Key Lab of Material Chemistry for Energy Conversion and Storage of Ministry of Education (HUST), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
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36
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Appeldorn JH, Lemcke S, Speck T, Nikoubashman A. Employing Artificial Neural Networks to Identify Reaction Coordinates and Pathways for Self-Assembly. J Phys Chem B 2022; 126:5007-5016. [DOI: 10.1021/acs.jpcb.2c02232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jörn H. Appeldorn
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Simon Lemcke
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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37
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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: 11] [Impact Index Per Article: 5.5] [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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38
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Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
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Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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39
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Tyukodi B, Mohajerani F, Hall DM, Grason GM, Hagan MF. Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries. ACS NANO 2022; 16:9077-9085. [PMID: 35638478 PMCID: PMC10362403 DOI: 10.1021/acsnano.2c00865] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration. The results determine the parameter range where finite-temperature self-limiting assembly occurs, in which the equilibrium assembly size distribution is sharply peaked around a well-defined finite size. The simulations also identify two mechanisms by which the system can escape frustration and assemble to unlimited size, and determine the particle-scale properties of subunits that suppress unbounded growth.
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Affiliation(s)
- Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Farzaneh Mohajerani
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
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40
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Pak A, Gupta M, Yeager M, Voth GA. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly toward Kinetically Trapped Morphologies. J Am Chem Soc 2022; 144:10417-10428. [PMID: 35666943 PMCID: PMC9204763 DOI: 10.1021/jacs.2c02568] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
During the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.
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Affiliation(s)
- Alexander
J. Pak
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Manish Gupta
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Mark Yeager
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States,Center
for Membrane Biology, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States, United States,Cardiovascular
Research Center, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States,Department
of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States,E-mail:
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41
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Zhou K, Mei Z, Lei Y, Guan Z, Mao C, Li Y. Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement. Chembiochem 2022; 23:e202200138. [PMID: 35676202 DOI: 10.1002/cbic.202200138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/08/2022] [Indexed: 11/11/2022]
Abstract
Cations such as divalent magnesium ion (Mg2+ ) play an essential role in DNA self-assembly. However, the strong electrostatic shielding effect of Mg2+ would be disadvantageous in some situations that require relatively weak interactions to allow a highly reversible error-correcting mechanism in the process of assembly. Herein, by substituting the conventional divalent Mg2+ with monovalent sodium ion (Na+ ), we have achieved one-pot high-yield assembly of tile-based DNA polyhedra at micromolar concentration of tiles, at least 10 times higher than the DNA concentrations reported previously. This strategy takes advantage of coexisting counterions and is expected to surmount the major obstacle to potential applications of such DNA nanostructures: large-scale production.
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Affiliation(s)
- Kaixuan Zhou
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhichao Mei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Yunxiang Lei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhen Guan
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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42
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Yang X, Lu ZY. Nanoparticle cluster formation mechanisms elucidated via Markov state modeling: Attraction range effects, aggregation pathways, and counterintuitive transition rates. J Chem Phys 2022; 156:214902. [DOI: 10.1063/5.0086110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanoparticle clusters are promising candidates for developing functional materials. However, it is still a challenging task to fabricate them in a predictable and controllable way, which requires investigation of the possible mechanisms underlying cluster formation at the nanoscale. By constructing Markov state models (MSMs) at the microstate level, we find that for highly dispersed particles to form a highly aggregated cluster, there are multiple coexisting pathways, which correspond to direct aggregation, or pathways that need to pass through partially aggregated, intermediate states. Varying the range of attraction between nanoparticles is found to significantly affect pathways. As the attraction range becomes narrower, compared to direct aggregation, some pathways that need to pass through partially aggregated intermediate states become more competitive. In addition, from MSMs constructed at the macrostate level, the aggregation rate is found to be counterintuitively lower with a lower free-energy barrier, which is also discussed.
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Affiliation(s)
- Xi Yang
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
| | - Zhong-Yuan Lu
- Institute of Theoretical Chemistry, State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130021, China
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43
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Feng J, Qiu Y, Jiang L, Wu Y. Long-Range-Ordered Assembly of Micro-/Nanostructures at Superwetting Interfaces. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106857. [PMID: 34908188 DOI: 10.1002/adma.202106857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/03/2021] [Indexed: 06/14/2023]
Abstract
On-chip integration of solution-processable materials imposes stringent and simultaneous requirements of controlled nucleation and growth, tunable geometry and dimensions, and long-range-ordered assembly, which is challenging in solution process far from thermodynamic equilibrium. Superwetting interfaces, underpinned by programmable surface chemistry and topography, are promising for steering transport, dewetting, and microfluid dynamics of liquids, thus opening a new paradigm for micro-/nanostructure assembly in solution process. Herein, assembly methods on the basis of superwetting interfaces are reviewed for constructing long-range-ordered micro-/nanostructures. Confined capillary liquids, including capillary bridges and capillary corner menisci realized by controlling local wettability and surface topography, are highlighted for simultaneously attained deterministic patterning and long-range order. The versatility and robustness of confined capillary liquids are discussed with assembly of single-crystalline micro-/nanostructures of organic semiconductors, metal-halide perovskites, and colloidal-nanoparticle superlattices, which lead to enhanced device performances and exotic functionalities. Finally, a perspective for promising directions in this realm is provided.
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Affiliation(s)
- Jiangang Feng
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Department of Chemical and Biomolecular Sciences, National University of Singapore, Singapore, 117585, Singapore
| | - Yuchen Qiu
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Yuchen Wu
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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44
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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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45
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Self-assembly and photoinduced fabrication of conductive nanographene wires on boron nitride. Nat Commun 2022; 13:442. [PMID: 35064113 PMCID: PMC8782843 DOI: 10.1038/s41467-021-27600-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/17/2021] [Indexed: 11/12/2022] Open
Abstract
Manufacturing molecule-based functional elements directly at device interfaces is a frontier in bottom-up materials engineering. A longstanding challenge in the field is the covalent stabilization of pre-assembled molecular architectures to afford nanodevice components. Here, we employ the controlled supramolecular self-assembly of anthracene derivatives on a hexagonal boron nitride sheet, to generate nanographene wires through photo-crosslinking and thermal annealing. Specifically, we demonstrate µm-long nanowires with an average width of 200 nm, electrical conductivities of 106 S m−1 and breakdown current densities of 1011 A m−2. Joint experiments and simulations reveal that hierarchical self-assembly promotes their formation and functional properties. Our approach demonstrates the feasibility of combined bottom-up supramolecular templating and top-down manufacturing protocols for graphene nanomaterials and interconnects, towards integrated carbon nanodevices. The bottom-up fabrication of structures with robust performance in the nm-to-μm scale usable for integrated carbon nanodevices is challenging. Here the authors report micrometer-long, highly conducting nanographene wires following self-assembly, photo-crosslinking and thermal annealing of anthracene derivatives on hexagonal boron nitride sheets.
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46
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Beeler C, Yahorau U, Coles R, Mills K, Whitelam S, Tamblyn I. Optimizing thermodynamic trajectories using evolutionary and gradient-based reinforcement learning. Phys Rev E 2022; 104:064128. [PMID: 35030917 DOI: 10.1103/physreve.104.064128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/24/2021] [Indexed: 11/07/2022]
Abstract
Using a model heat engine, we show that neural-network-based reinforcement learning can identify thermodynamic trajectories of maximal efficiency. We consider both gradient and gradient-free reinforcement learning. We use an evolutionary learning algorithm to evolve a population of neural networks, subject to a directive to maximize the efficiency of a trajectory composed of a set of elementary thermodynamic processes; the resulting networks learn to carry out the maximally efficient Carnot, Stirling, or Otto cycles. When given an additional irreversible process, this evolutionary scheme learns a previously unknown thermodynamic cycle. Gradient-based reinforcement learning is able to learn the Stirling cycle, whereas an evolutionary approach achieves the optimal Carnot cycle. Our results show how the reinforcement learning strategies developed for game playing can be applied to solve physical problems conditioned upon path-extensive order parameters.
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Affiliation(s)
- Chris Beeler
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5.,National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6
| | - Uladzimir Yahorau
- Department of Physics, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1G 0C5
| | - Rory Coles
- Department of Physics and Astronomy, University of Victoria, Victoria, British Columbia, Canada V8P 5C2
| | - Kyle Mills
- Department of Physics, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1G 0C5.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada M5G 1M1
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isaac Tamblyn
- Department of Physics, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1G 0C5.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada M5G 1M1.,Department of Physics, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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47
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Wang M, Park C, Woehl TJ. Real-time imaging of metallic supraparticle assembly during nanoparticle synthesis. NANOSCALE 2022; 14:312-319. [PMID: 34928292 DOI: 10.1039/d1nr05416c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Observations of nanoparticle superlattice formation over minutes during colloidal nanoparticle synthesis elude description by conventional understanding of self-assembly, which theorizes superlattices require extended formation times to allow for diffusively driven annealing of packing defects. It remains unclear how nanoparticle position annealing occurs on such short time scales despite the rapid superlattice growth kinetics. Here we utilize liquid phase transmission electron microscopy to directly image the self-assembly of platinum nanoparticles into close packed supraparticles over tens of seconds during nanoparticle synthesis. Electron-beam induced reduction of an aqueous platinum precursor formed monodisperse 2-3 nm platinum nanoparticles that simultaneously self-assembled over tens of seconds into 3D supraparticles, some of which showed crystalline ordered domains. Experimentally varying the interparticle interactions (e.g., electrostatic, steric interactions) by changing precursor chemistry revealed that supraparticle formation was driven by weak attractive van der Waals forces balanced by short ranged repulsive steric interactions. Growth kinetic measurements and an interparticle interaction model demonstrated that nanoparticle surface diffusion rates on the supraparticles were orders of magnitude faster than nanoparticle attachment, enabling nanoparticles to find high coordination binding sites unimpeded by incoming particles. These results reconcile rapid self-assembly of supraparticles with the conventional self-assembly paradigm in which nanocrystal position annealing by surface diffusion occurs on a significantly shorter time scale than nanocrystal attachment.
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Affiliation(s)
- Mei Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA.
| | - Chiwoo Park
- Department of Industrial and Manufacturing Engineering, Florida State University, Tallahassee, FL, USA
| | - Taylor J Woehl
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA.
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48
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Ben-Ari A, Ben-Ari L, Bisker G. Nonequilibrium self-assembly of multiple stored targets in a dimer-based system. J Chem Phys 2021; 155:234113. [PMID: 34937365 DOI: 10.1063/5.0069161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nonequilibrium self-assembly can be found in various biological processes where chemical potential gradients are exploited to steer the system to a desired organized structure with a particular function. Microtubules, for example, are composed of two globular protein subunits, α-tubulin and β-tubulin, which bind together to form polar dimers that self-assemble a hollow cylinder structure in a process driven by GTPase activity. Inspired by this process, we define a generic self-assembly lattice model containing particles of two subunits, which is driven out-of-equilibrium by a dimer-favoring local driving force. Using Monte Carlo simulations, we characterize the ability of this system to restore pre-encoded target structures as a function of the initial seed size, interaction energy, chemical potential, number of target structures, and strength of the nonequilibrium drive. We demonstrate some intriguing consequences of the drive, such as a smaller critical seed and an improved target assembly stability, compared to the equilibrium scenario. Our results can expand the theoretical basis of nonequilibrium self-assembly and provide deeper understanding of how nonequilibrium driving can overcome equilibrium constraints.
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Affiliation(s)
- Adi Ben-Ari
- Faculty of Engineering, School of Electrical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liron Ben-Ari
- Faculty of Engineering, School of Electrical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Faculty of Engineering, Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
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49
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Royall CP, Faers MA, Fussell SL, Hallett JE. Real space analysis of colloidal gels: triumphs, challenges and future directions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:453002. [PMID: 34034239 DOI: 10.1088/1361-648x/ac04cb] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Colloidal gels constitute an important class of materials found in many contexts and with a wide range of applications. Yet as matter far from equilibrium, gels exhibit a variety of time-dependent behaviours, which can be perplexing, such as an increase in strength prior to catastrophic failure. Remarkably, such complex phenomena are faithfully captured by an extremely simple model-'sticky spheres'. Here we review progress in our understanding of colloidal gels made through the use of real space analysis and particle resolved studies. We consider the challenges of obtaining a suitable experimental system where the refractive index and density of the colloidal particles is matched to that of the solvent. We review work to obtain a particle-level mechanism for rigidity in gels and the evolution of our understanding of time-dependent behaviour, from early-time aggregation to ageing, before considering the response of colloidal gels to deformation and then move on to more complex systems of anisotropic particles and mixtures. Finally we note some more exotic materials with similar properties.
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Affiliation(s)
- C Patrick Royall
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
- HH Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
- School of Chemistry, University of Bristol, Cantock Close, Bristol, BS8 1TS, United Kingdom
- Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol, BS8 1FD, United Kingdom
| | - Malcolm A Faers
- Bayer AG, Crop Science Division, Formulation Technology, Alfred Nobel Str. 50, 40789 Monheim, Germany
| | - Sian L Fussell
- School of Chemistry, University of Bristol, Cantock Close, Bristol, BS8 1TS, United Kingdom
- Bristol Centre for Functional Nanomaterials, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - James E Hallett
- Physical and Theoretical Chemistry Laboratory, South Parks Road, University of Oxford, OX1 3QZ, United Kingdom
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50
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Dissanayake TU, Wang M, Woehl TJ. Revealing Reactions between the Electron Beam and Nanoparticle Capping Ligands with Correlative Fluorescence and Liquid-Phase Electron Microscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:37553-37562. [PMID: 34338503 DOI: 10.1021/acsami.1c10957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Liquid-phase transmission electron microscopy (LP-TEM) enables real-time imaging of nanoparticle self-assembly, formation, and etching with single nanometer resolution. Despite the importance of organic nanoparticle capping ligands in these processes, the effect of electron beam irradiation on surface-bound and soluble capping ligands during LP-TEM imaging has not been investigated. Here, we use correlative LP-TEM and fluorescence microscopy (FM) to demonstrate that polymeric nanoparticle ligands undergo competing crosslinking and chain scission reactions that nonmonotonically modify ligand coverage over time. Branched polyethylenimine (BPEI)-coated silver nanoparticles were imaged with dose-controlled LP-TEM followed by labeling their primary amine groups with fluorophores to visualize the local thickness of adsorbed capping ligands. FM images showed that free ligands crosslinked in the LP-TEM image area over imaging times of tens of seconds, enhancing local capping ligand coverage on nanoparticles and silicon nitride membranes. Nanoparticle surface ligands underwent chain scission over irradiation times of minutes to tens of minutes, which depleted surface ligands from the nanoparticle and silicon nitride surface. Conversely, solutions of only soluble capping ligand underwent successive crosslinking reactions with no chain scission, suggesting that nanoparticles enhanced the chain scission reactions by acting as radiolysis hotspots. The addition of a hydroxyl radical scavenger, tert-butanol, eliminated chain scission reactions and slowed the progression of crosslinking reactions. These experiments have important implications for performing controlled and reproducible LP-TEM nanoparticle imaging as they demonstrate that the electron beam can significantly alter ligand coverage on nanoparticles in a nonintuitive manner. They emphasize the need to understand and control the electron beam radiation chemistry of a given sample to avoid significant perturbations to the nanoparticle capping ligand chemistry, which are invisible in electron micrographs.
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Affiliation(s)
- Thilini U Dissanayake
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, College Park, Maryland 20742, United States
| | - Mei Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, College Park, Maryland 20742, United States
| | - Taylor J Woehl
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, College Park, Maryland 20742, United States
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