1
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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024; 18:14791-14840. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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2
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Lizano A, Tang X. Convolutional neural network-based colloidal self-assembly state classification. SOFT MATTER 2023; 19:3450-3457. [PMID: 37129254 DOI: 10.1039/d3sm00139c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Colloidal self-assembly is a viable solution to making advanced metamaterials. While the physicochemical properties of the particles affect the properties of the assembled structures, particle configuration is also a critical determinant factor. Colloidal self-assembly state classification is typically achieved with order parameters, which are aggregate variables normally defined with nontrivial exploration and validation. Here, we present an image-based framework to classify the state of a 2-D colloidal self-assembly system. The framework leverages deep learning algorithms with unsupervised learning for state classification and a supervised learning-based convolutional neural network for state prediction. The neural network models are developed using data from an experimentally validated Brownian dynamics simulation. Our results demonstrate that the proposed approach gives a satisfying performance, comparable and even outperforming the commonly used order parameters in distinguishing void defective states from ordered states. Given the data-based nature of the approach, we anticipate its general applicability and potential automatability to different and complex systems where image or particle coordination acquisition is feasible.
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Affiliation(s)
- Andres Lizano
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
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3
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Altman LE, Grier DG. Machine learning enables precise holographic characterization of colloidal materials in real time. SOFT MATTER 2023; 19:3002-3014. [PMID: 37017639 DOI: 10.1039/d2sm01283a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Holographic particle characterization uses in-line holographic video microscopy to track and characterize individual colloidal particles dispersed in their native fluid media. Applications range from fundamental research in statistical physics to product development in biopharmaceuticals and medical diagnostic testing. The information encoded in a hologram can be extracted by fitting to a generative model based on the Lorenz-Mie theory of light scattering. Treating hologram analysis as a high-dimensional inverse problem has been exceptionally successful, with conventional optimization algorithms yielding nanometer precision for a typical particle's position and part-per-thousand precision for its size and index of refraction. Machine learning previously has been used to automate holographic particle characterization by detecting features of interest in multi-particle holograms and estimating the particles' positions and properties for subsequent refinement. This study presents an updated end-to-end neural-network solution called CATCH (Characterizing and Tracking Colloids Holographically) whose predictions are fast, precise, and accurate enough for many real-world high-throughput applications and can reliably bootstrap conventional optimization algorithms for the most demanding applications. The ability of CATCH to learn a representation of Lorenz-Mie theory that fits within a diminutive 200 kB hints at the possibility of developing a greatly simplified formulation of light scattering by small objects.
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Affiliation(s)
- Lauren E Altman
- Department of Physics and Center for Soft Matter Research, New York University, New York, NY 10003, USA.
| | - David G Grier
- Department of Physics and Center for Soft Matter Research, New York University, New York, NY 10003, USA.
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4
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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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5
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Mao R, O’Leary J, Mesbah A, Mittal J. A Deep Learning Framework Discovers Compositional Order and Self-Assembly Pathways in Binary Colloidal Mixtures. JACS AU 2022; 2:1818-1828. [PMID: 36032540 PMCID: PMC9400045 DOI: 10.1021/jacsau.2c00111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Binary colloidal superlattices (BSLs) have demonstrated enormous potential for the design of advanced multifunctional materials that can be synthesized via colloidal self-assembly. However, mechanistic understanding of the three-dimensional self-assembly of BSLs is largely limited due to a lack of tractable strategies for characterizing the many two-component structures that can appear during the self-assembly process. To address this gap, we present a framework for colloidal crystal structure characterization that uses branched graphlet decomposition with deep learning to systematically and quantitatively describe the self-assembly of BSLs at the single-particle level. Branched graphlet decomposition is used to evaluate local structure via high-dimensional neighborhood graphs that quantify both structural order (e.g., body-centered-cubic vs face-centered-cubic) and compositional order (e.g., substitutional defects) of each individual particle. Deep autoencoders are then used to efficiently translate these neighborhood graphs into low-dimensional manifolds from which relationships among neighborhood graphs can be more easily inferred. We demonstrate the framework on in silico systems of DNA-functionalized particles, in which two well-recognized design parameters, particle size ratio and interparticle potential well depth can be adjusted independently. The framework reveals that binary colloidal mixtures with small interparticle size disparities (i.e., A- and B-type particle radius ratios of r A/r B = 0.8 to r A/r B = 0.95) can promote the self-assembly of defect-free BSLs much more effectively than systems of identically sized particles, as nearly defect-free BCC-CsCl, FCC-CuAu, and IrV crystals are observed in the former case. The framework additionally reveals that size-disparate colloidal mixtures can undergo nonclassical nucleation pathways where BSLs evolve from dense amorphous precursors, instead of directly nucleating from dilute solution. These findings illustrate that the presented characterization framework can assist in enhancing mechanistic understanding of the self-assembly of binary colloidal mixtures, which in turn can pave the way for engineering the growth of defect-free BSLs.
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Affiliation(s)
- Runfang Mao
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jared O’Leary
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ali Mesbah
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Jeetain Mittal
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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6
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Kadupitiya JCS, Fox GC, Jadhao V. Solving Newton’s equations of motion with large timesteps using recurrent neural networks based operators. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1088/2632-2153/ac5f60] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Classical molecular dynamics simulations are based on solving Newton’s equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton’s equations. We introduce operators derived using recurrent neural networks that accurately solve Newton’s equations utilizing sequences of past trajectory data, and produce energy-conserving dynamics of particles using timesteps up to 4000 times larger compared to the Verlet timestep. We demonstrate significant speedup in many example problems including 3D systems of up to 16 particles.
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7
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Machine-Learned Free Energy Surfaces for Capillary Condensation and Evaporation in Mesopores. ENTROPY 2022; 24:e24010097. [PMID: 35052123 PMCID: PMC8774451 DOI: 10.3390/e24010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 12/04/2022]
Abstract
Using molecular simulations, we study the processes of capillary condensation and capillary evaporation in model mesopores. To determine the phase transition pathway, as well as the corresponding free energy profile, we carry out enhanced sampling molecular simulations using entropy as a reaction coordinate to map the onset of order during the condensation process and of disorder during the evaporation process. The structural analysis shows the role played by intermediate states, characterized by the onset of capillary liquid bridges and bubbles. We also analyze the dependence of the free energy barrier on the pore width. Furthermore, we propose a method to build a machine learning model for the prediction of the free energy surfaces underlying capillary phase transition processes in mesopores.
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8
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Statt A, Kleeblatt DC, Reinhart WF. Unsupervised learning of sequence-specific aggregation behavior for a model copolymer. SOFT MATTER 2021; 17:7697-7707. [PMID: 34350929 DOI: 10.1039/d1sm01012c] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We apply a recently developed unsupervised machine learning scheme for local environments [Reinhart, Comput. Mater. Sci., 2021, 196, 110511] to characterize large-scale, disordered aggregates formed by sequence-defined macromolecules. This method provides new insight into the structure of these disordered, dilute aggregates, which has proven difficult to understand using collective variables manually derived from expert knowledge [Statt et al., J. Chem. Phys., 2020, 152, 075101]. In contrast to such conventional order parameters, we are able to classify the global aggregate structure directly using descriptions of the local environments. The resulting characterization provides a deeper understanding of the range of possible self-assembled structures and their relationships to each other. We also provide detailed analysis of the effects of finite system size, stochasticity, and kinetics of these aggregates based on the learned collective variables. Interestingly, we find that the spatiotemporal evolution of systems in the learned latent space is smooth and continuous, despite being derived from only a single snapshot from each of about 1000 monomer sequences. These results demonstrate the insight which can be gained by applying unsupervised machine learning to soft matter systems, especially when suitable order parameters are not known.
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Affiliation(s)
- Antonia Statt
- Materials Science and Engineering, Grainger College of Engineering, University of Illinois, Urbana-Champaign, IL 61801, USA
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9
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Abstract
Machine learning is making a major impact in materials research. I review current progress across a selection of areas of ubiquitous soft matter. When applied to particle tracking, machine learning using convolution neural networks is providing impressive performance but there remain some significant problems to solve. Characterising ordered arrangements of particles is a huge challenge and machine learning has been deployed to create the description, perform the classification and tease out an interpretation using a wide array of techniques often with good success. In glass research, machine learning has proved decisive in quantifying very subtle correlations between the local structure around a site and the susceptibility towards a rearrangement event at that site. There are also beginning to be some impressive attempts to deploy machine learning in the design of composite soft materials. The discovery aspect of this new materials design meets the current interest in teaching algorithms to learn to extrapolate beyond the training data.
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Affiliation(s)
- Paul S Clegg
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK.
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10
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O'Leary J, Mao R, Pretti EJ, Paulson JA, Mittal J, Mesbah A. Deep learning for characterizing the self-assembly of three-dimensional colloidal systems. SOFT MATTER 2021; 17:989-999. [PMID: 33284930 DOI: 10.1039/d0sm01853h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Creating a systematic framework to characterize the structural states of colloidal self-assembly systems is crucial for unraveling the fundamental understanding of these systems' stochastic and non-linear behavior. The most accurate characterization methods create high-dimensional neighborhood graphs that may not provide useful information about structures unless these are well-defined reference crystalline structures. Dimensionality reduction methods are thus required to translate the neighborhood graphs into a low-dimensional space that can be easily interpreted and used to characterize non-reference structures. We investigate a framework for colloidal system state characterization that employs deep learning methods to reduce the dimensionality of neighborhood graphs. The framework next uses agglomerative hierarchical clustering techniques to partition the low-dimensional space and assign physically meaningful classifications to the resulting partitions. We first demonstrate the proposed colloidal self-assembly state characterization framework on a three-dimensional in silico system of 500 multi-flavored colloids that self-assemble under isothermal conditions. We next investigate the generalizability of the characterization framework by applying the framework to several independent self-assembly trajectories, including a three-dimensional in silico system of 2052 colloidal particles that undergo evaporation-induced self-assembly.
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Affiliation(s)
- Jared O'Leary
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
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11
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Das A, Limmer DT. Variational design principles for nonequilibrium colloidal assembly. J Chem Phys 2021; 154:014107. [DOI: 10.1063/5.0038652] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94609, USA
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, California 94609, USA
- Kavli Energy NanoScience Institute, Berkeley, California 94609, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94609, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94609, USA
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12
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Borrelli E, Parravano M, Sacconi R, Costanzo E, Querques L, Vella G, Bandello F, Querques G. Guidelines on Optical Coherence Tomography Angiography Imaging: 2020 Focused Update. Ophthalmol Ther 2020; 9:697-707. [PMID: 32740741 PMCID: PMC7708612 DOI: 10.1007/s40123-020-00286-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
Optical coherence tomography angiography (OCTA) has significantly expanded our knowledge of the ocular vasculature. In this review, we provide a discussion of the fundamental principles of OCTA and the application of this imaging modality to study the retinal and choroidal vessels. These guidelines are focused on 2020, and include updates since the 2019 publication. Importantly, we will comment on recent findings on OCTA technology with a special focus on the three-dimensional (3D) OCTA visualization.
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Affiliation(s)
- Enrico Borrelli
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
| | | | - Riccardo Sacconi
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
| | | | - Lea Querques
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
| | - Giovanna Vella
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
- Ophthalmology, Department of Surgical, Medical, Molecular Pathology and of Critical Area, University of Pisa, Pisa, Italy
| | - Francesco Bandello
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
| | - Giuseppe Querques
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy.
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13
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Pattern detection in colloidal assembly: A mosaic of analysis techniques. Adv Colloid Interface Sci 2020; 284:102252. [PMID: 32971396 DOI: 10.1016/j.cis.2020.102252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 01/19/2023]
Abstract
Characterization of the morphology, identification of patterns and quantification of order encountered in colloidal assemblies is essential for several reasons. First of all, it is useful to compare different self-assembly methods and assess the influence of different process parameters on the final colloidal pattern. In addition, casting light on the structures formed by colloidal particles can help to get better insight into colloidal interactions and understand phase transitions. Finally, the growing interest in colloidal assemblies in materials science for practical applications going from optoelectronics to biosensing imposes a thorough characterization of the morphology of colloidal assemblies because of the intimate relationship between morphology and physical properties (e.g. optical and mechanical) of a material. Several image analysis techniques developed to investigate images (acquired via scanning electron microscopy, digital video microscopy and other imaging methods) provide variegated and complementary information on the colloidal structures under scrutiny. However, understanding how to use such image analysis tools to get information on the characteristics of the colloidal assemblies may represent a non-trivial task, because it requires the combination of approaches drawn from diverse disciplines such as image processing, computational geometry and computational topology and their application to a primarily physico-chemical process. Moreover, the lack of a systematic description of such analysis tools makes it difficult to select the ones more suitable for the features of the colloidal assembly under examination. In this review we provide a methodical and extensive description of real-space image analysis tools by explaining their principles and their application to the investigation of two-dimensional colloidal assemblies with different morphological characteristics.
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14
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Culha U, Davidson ZS, Mastrangeli M, Sitti M. Statistical reprogramming of macroscopic self-assembly with dynamic boundaries. Proc Natl Acad Sci U S A 2020; 117:11306-11313. [PMID: 32385151 PMCID: PMC7260983 DOI: 10.1073/pnas.2001272117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Self-assembly is a ubiquitous process that can generate complex and functional structures via local interactions among a large set of simpler components. The ability to program the self-assembly pathway of component sets elucidates fundamental physics and enables alternative competitive fabrication technologies. Reprogrammability offers further opportunities for tuning structural and material properties but requires reversible selection from multistable self-assembling patterns, which remains a challenge. Here, we show statistical reprogramming of two-dimensional (2D), noncompact self-assembled structures by the dynamic confinement of orbitally shaken and magnetically repulsive millimeter-scale particles. Under a constant shaking regime, we control the rate of radius change of an assembly arena via moving hard boundaries and select among a finite set of self-assembled patterns repeatably and reversibly. By temporarily trapping particles in topologically identified stable states, we also demonstrate 2D reprogrammable stiffness and three-dimensional (3D) magnetic clutching of the self-assembled structures. Our reprogrammable system has prospective implications for the design of granular materials in a multitude of physical scales where out-of-equilibrium self-assembly can be realized with different numbers or types of particles. Our dynamic boundary regulation may also enable robust bottom-up control strategies for novel robotic assembly applications by designing more complex spatiotemporal interactions using mobile robots.
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Affiliation(s)
- Utku Culha
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Zoey S Davidson
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Massimo Mastrangeli
- Electronic Components, Technology and Materials, Department of Microelectronics, Delft University of Technology, 2628CT Delft, The Netherlands
| | - Metin Sitti
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany;
- School of Medicine and School of Engineering, Koç University, 34450 Istanbul, Turkey
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15
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Whitelam S, Tamblyn I. Learning to grow: Control of material self-assembly using evolutionary reinforcement learning. Phys Rev E 2020; 101:052604. [PMID: 32575260 DOI: 10.1103/physreve.101.052604] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential in order to promote the assembly of desired structures or choose between competing polymorphs. In the first case, networks reproduce in a qualitative sense the results of previously known protocols, but faster and with higher fidelity; in the second case they identify strategies previously unknown, from which we can extract physical insight. Networks that take as input the elapsed time of the simulation or microscopic information from the system are both effective, the latter more so. The evolutionary scheme we have used is simple to implement and can be applied to a broad range of examples of experimental self-assembly, whether or not one can monitor the experiment as it proceeds. Our results have been achieved with no human input beyond the specification of which order parameter to promote, pointing the way to the design of synthesis protocols by artificial intelligence.
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Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Isaac Tamblyn
- National Research Council of Canada, Ottawa, Ontario, Canada and Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
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16
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Huang S, Quevillon MJ, Kyhl S, Whitmer JK. Surveying the free energy landscape of clusters of attractive colloidal spheres. J Chem Phys 2020; 152:134901. [PMID: 32268752 DOI: 10.1063/1.5144984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Controlling the assembly of colloidal particles into specific structures has been a long-term goal of the soft materials community. Much can be learned about the process of self-assembly by examining the early stage assembly into clusters. For the simple case of hard spheres with short-range attractions, the rigid clusters of N particles (where N is small) have been enumerated theoretically and tested experimentally. Less is known, however, about how the free energy landscapes are altered when the inter-particle potential is long-ranged. In this work, we demonstrate how adaptive biasing in molecular simulations may be used to pinpoint shifts in the stability of colloidal clusters as the inter-particle potential is varied. We also discuss the generality of our techniques and strategies for application to related molecular systems.
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Affiliation(s)
- Shanghui Huang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Michael J Quevillon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Soren Kyhl
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jonathan K Whitmer
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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17
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Borrelli E, Viggiano P, Evangelista F, Toto L, Mastropasqua R. Eyelashes Artifact in Ultra-Widefield Optical Coherence Tomography Angiography. Ophthalmic Surg Lasers Imaging Retina 2020; 50:740-743. [PMID: 31755975 DOI: 10.3928/23258160-20191031-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND OBJECTIVE To describe the presence of eyelashes artifact in ultra-widefield swept-source optical coherence tomography angiography (SS-OCTA) images. PATIENTS AND METHODS In this prospective, cross-sectional study, 52 healthy, young subjects were imaged with the SS-OCTA system. OCTA scans were taken in primary and extremes of gaze, and a montage was automatically created. The en face choriocapillaris images were then exported, and a semi-automated algorithm was used for subsequent quantitative analysis. RESULTS The authors noted the presence of some linear regions of reduced brightness, which were assumed to represent a shadow effect due to patient eyelashes. In order to quantify this effect, the authors performed a quantitative analysis of the superior and inferior regions in the retinal and choroidal vessels. CONCLUSIONS The authors' qualitative and quantitative analysis showed the presence of regions of false-positive hypoperfusion secondary to eyelashes artifacts. To the authors' knowledge, this represents the first description of this new type of shadowing artifact affecting OCTA images. [Ophthalmic Surg Lasers Imaging Retina. 2019;50:740-743.].
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18
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Bejagam KK, Singh SK, Ahn R, Deshmukh SA. Unraveling the Conformations of Backbone and Side Chains in Thermosensitive Bottlebrush Polymers. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Karteek K. Bejagam
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Rebecca Ahn
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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19
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Borrelli E, Sadda SR, Uji A, Querques G. Pearls and Pitfalls of Optical Coherence Tomography Angiography Imaging: A Review. Ophthalmol Ther 2019; 8:215-226. [PMID: 30868418 PMCID: PMC6513942 DOI: 10.1007/s40123-019-0178-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 12/28/2022] Open
Abstract
Optical coherence tomography angiography (OCTA) has significantly expanded our knowledge of the ocular vasculature. Furthermore, this imaging modality has been widely adopted to investigate different ocular and systemic diseases. In this review, a discussion of the fundamental principles of OCTA is followed by the application of this imaging modality to study the retinal and choroidal vessels. A proper comprehension of this imaging modality is essential for the interpretation of OCTA imaging applications in retinal and choroidal disorders.
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Affiliation(s)
- Enrico Borrelli
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy
| | - SriniVas R Sadda
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Doheny Eye Institute, Los Angeles, CA, USA
| | - Akihito Uji
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Giuseppe Querques
- Ophthalmology Department, San Raffaele University Hospital, Milan, Italy.
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20
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Coughlan ACH, Torres-Díaz I, Zhang J, Bevan MA. Non-equilibrium steady-state colloidal assembly dynamics. J Chem Phys 2019; 150:204902. [PMID: 31153195 DOI: 10.1063/1.5094554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Simulations and experiments are reported for nonequilibrium steady-state assembly of small colloidal crystal clusters in rotating magnetic fields vs frequency and amplitude. High-dimensional trajectories of particle coordinates from image analysis of experiments and from Stokesian Dynamic computer simulations are fit to low-dimensional reaction coordinate based Fokker-Planck and Langevin equations. The coefficients of these equations are effective energy and diffusivity landscapes that capture configuration-dependent energy and friction for nonequilibrium steady-state dynamics. Two reaction coordinates that capture condensation and anisotropy of dipolar chains folding into crystals are sufficient to capture high-dimensional experimental and simulated dynamics in terms of first passage time distributions. Our findings illustrate how field-mediated nonequilibrium steady-state colloidal assembly dynamics can be modeled to interpret and design pathways toward target microstructures and morphologies.
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Affiliation(s)
- Anna C H Coughlan
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Isaac Torres-Díaz
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Jianli Zhang
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Michael A Bevan
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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21
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Lee EY, Zhang C, Di Domizio J, Jin F, Connell W, Hung M, Malkoff N, Veksler V, Gilliet M, Ren P, Wong GCL. Helical antimicrobial peptides assemble into protofibril scaffolds that present ordered dsDNA to TLR9. Nat Commun 2019; 10:1012. [PMID: 30833557 PMCID: PMC6399285 DOI: 10.1038/s41467-019-08868-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/27/2018] [Indexed: 01/14/2023] Open
Abstract
Amphiphilicity in ɑ-helical antimicrobial peptides (AMPs) is recognized as a signature of potential membrane activity. Some AMPs are also strongly immunomodulatory: LL37-DNA complexes potently amplify Toll-like receptor 9 (TLR9) activation in immune cells and exacerbate autoimmune diseases. The rules governing this proinflammatory activity of AMPs are unknown. Here we examine the supramolecular structures formed between DNA and three prototypical AMPs using small angle X-ray scattering and molecular modeling. We correlate these structures to their ability to activate TLR9 and show that a key criterion is the AMP's ability to assemble into superhelical protofibril scaffolds. These structures enforce spatially-periodic DNA organization in nanocrystalline immunocomplexes that trigger strong recognition by TLR9, which is conventionally known to bind single DNA ligands. We demonstrate that we can "knock in" this ability for TLR9 amplification in membrane-active AMP mutants, which suggests the existence of tradeoffs between membrane permeating activity and immunomodulatory activity in AMP sequences.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Jeremy Di Domizio
- Department of Dermatology, Lausanne University Hospital CHUV, 1011, Lausanne, Switzerland
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Will Connell
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mandy Hung
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nicolas Malkoff
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Veronica Veksler
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michel Gilliet
- Department of Dermatology, Lausanne University Hospital CHUV, 1011, Lausanne, Switzerland
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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22
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Borrelli E, Sarraf D, Freund KB, Sadda SR. OCT angiography and evaluation of the choroid and choroidal vascular disorders. Prog Retin Eye Res 2018; 67:30-55. [DOI: 10.1016/j.preteyeres.2018.07.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/31/2022]
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23
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Mansbach RA, Ferguson AL. Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides. J Phys Chem B 2018; 122:10219-10236. [DOI: 10.1021/acs.jpcb.8b05781] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rachael A. Mansbach
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana−Champaign, 1304 W Green Street, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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24
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Abstract
Optimizing force-field (FF) parameters to perform molecular dynamics (MD) simulations is a challenging and time-consuming process. We present a novel FF optimization framework that integrates MD simulations with particle swarm optimization (PSO) algorithm and artificial neural network (ANN). This new ANN-assisted PSO framework was used to develop transferable coarse-grained (CG) models for D2O and DMF as a proof of concept. The PSO algorithm was used to generate the set of input FF parameters for the MD simulations of the CG models of these solvents, which were optimized to reproduce their experimental properties. Herein, for the first time, a reverse approach was employed for on-the-fly training of the ANN model, where results (solvent properties) obtained from the MD simulations and their corresponding FF parameters were used as inputs and outputs, respectively. The ANN model was then required to predict a set of new FF parameters, which were tested for their ability to predict the desired experimental properties. This new framework can be extended to integrate any optimization algorithm with ANN and MD simulations to accelerate the FF development.
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Affiliation(s)
- Karteek K Bejagam
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Samrendra Singh
- CNH Industrial , Burr Ridge , Illinois 60527 , United States
| | - Yaxin An
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Sanket A Deshmukh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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25
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Reinhart WF, Panagiotopoulos AZ. Automated crystal characterization with a fast neighborhood graph analysis method. SOFT MATTER 2018; 14:6083-6089. [PMID: 29989134 DOI: 10.1039/c8sm00960k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a significantly improved, very fast implementation of the Neighborhood Graph Analysis technique for template-free characterization of crystal structures [W. F. Reinhart et al., Soft Matter, 2017, 13, 4733]. By comparing local neighborhoods in terms of their relative graphlet frequencies, we reduce the computational cost by four orders of magnitude compared to the original stochastic method. Furthermore, we present protocols for the detection of topologically important structures and assignment of visually informative colors, providing a fully automated procedure for characterization of crystal structures from particle tracking data. We demonstrate the flexibility of our method on a wide range of crystal structures which have proven difficult to classify by previously available techniques.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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26
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Wang J, Gayatri M, Ferguson AL. Coarse-Grained Molecular Simulation and Nonlinear Manifold Learning of Archipelago Asphaltene Aggregation and Folding. J Phys Chem B 2018; 122:6627-6647. [DOI: 10.1021/acs.jpcb.8b01634] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiang Wang
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Mohit Gayatri
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, Illinois 61801, United States
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27
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Zhang J, Luijten E, Grzybowski BA, Granick S. Active colloids with collective mobility status and research opportunities. Chem Soc Rev 2018; 46:5551-5569. [PMID: 28762406 DOI: 10.1039/c7cs00461c] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The collective mobility of active matter (self-propelled objects that transduce energy into mechanical work to drive their motion, most commonly through fluids) constitutes a new frontier in science and achievable technology. This review surveys the current status of the research field, what kinds of new scientific problems can be tackled in the short term, and what long-term directions are envisioned. We focus on: (1) attempts to formulate design principles to tailor active particles; (2) attempts to design principles according to which active particles interact under circumstances where particle-particle interactions of traditional colloid science are augmented by a family of nonequilibrium effects discussed here; (3) attempts to design intended patterns of collective behavior and dynamic assembly; (4) speculative links to equilibrium thermodynamics. In each aspect, we assess achievements, limitations, and research opportunities.
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Affiliation(s)
- Jie Zhang
- Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA
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28
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Ferguson AL. Machine learning and data science in soft materials engineering. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:043002. [PMID: 29111979 DOI: 10.1088/1361-648x/aa98bd] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In many branches of materials science it is now routine to generate data sets of such large size and dimensionality that conventional methods of analysis fail. Paradigms and tools from data science and machine learning can provide scalable approaches to identify and extract trends and patterns within voluminous data sets, perform guided traversals of high-dimensional phase spaces, and furnish data-driven strategies for inverse materials design. This topical review provides an accessible introduction to machine learning tools in the context of soft and biological materials by 'de-jargonizing' data science terminology, presenting a taxonomy of machine learning techniques, and surveying the mathematical underpinnings and software implementations of popular tools, including principal component analysis, independent component analysis, diffusion maps, support vector machines, and relative entropy. We present illustrative examples of machine learning applications in soft matter, including inverse design of self-assembling materials, nonlinear learning of protein folding landscapes, high-throughput antimicrobial peptide design, and data-driven materials design engines. We close with an outlook on the challenges and opportunities for the field.
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Affiliation(s)
- Andrew L Ferguson
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, United States of America. Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, United States of America. Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, United States of America. Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
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29
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Wang J, Ferguson AL. A Study of the Morphology, Dynamics, and Folding Pathways of Ring Polymers with Supramolecular Topological Constraints Using Molecular Simulation and Nonlinear Manifold Learning. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b01684] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiang Wang
- Department
of Physics, ‡Department of Materials Science and Engineering, and §Department of
Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department
of Physics, ‡Department of Materials Science and Engineering, and §Department of
Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
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30
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Wang J, Ferguson AL. Nonlinear machine learning in simulations of soft and biological materials. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1400164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- J. Wang
- Department of Physics, University of Illinois Urbana-Champaign , Urbana, IL, USA
| | - A. L. Ferguson
- Department of Physics, University of Illinois Urbana-Champaign , Urbana, IL, USA
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign , Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign , Urbana, IL, USA
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31
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Reinhart WF, Panagiotopoulos AZ. Multi-atom pattern analysis for binary superlattices. SOFT MATTER 2017; 13:6803-6809. [PMID: 28949366 DOI: 10.1039/c7sm01642e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a method for the template-free characterization of binary superlattices. This is an extension of the Neighborhood Graph Analysis method, a technique which evaluates relationships between observed structures based on the topology of their first coordination shell [W. F. Reinhart, et al., Soft Matter, 2017, 13, 4733]. In the present work, we develop a framework for the analysis of multi-atom patterns, which incorporate structural information from the second coordination shell while providing a unified signature for all constituent particles in the superlattice. We construct an efficient metric for making quantitative comparisons between these patterns, making our algorithm the first capable of characterizing partial or defective superlattice structures. As in our previous work, we leverage machine learning techniques to characterize a range of self-assembled crystal structures, discovering a set of emergent collective variables which map each observed pattern into an intuitive global phase space. We demonstrate the method by performing classification of configurations from simulations of binary colloidal self-assembly in two dimensions.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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32
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Zhang J, Grzybowski BA, Granick S. Janus Particle Synthesis, Assembly, and Application. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6964-6977. [PMID: 28678499 DOI: 10.1021/acs.langmuir.7b01123] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Janus particles are colloidal particles with more than a single type of surface chemistry or composition, ranging in size from hundreds of nanometers to a few micrometers. Like traditional colloids, they are large enough to be observed under optical microscopy in real time and small enough to diffuse by Brownian motion, but their interesting and useful new properties of directional interaction bring new research opportunities to the fields of soft matter and fundamental materials research as well as to applications in other disciplines and in technologies such as electronic paper and other multiphase engineering. In this review, a variety of methods that have been used to synthesize Janus particles are introduced. Following this, we summarize the use of Janus particles as basic units that assemble into novel structures and tune important material properties. The concluding sections highlight some of the technological applications, including recent progress in using Janus particles as microprobes, micromotors, electronic paper, and solid surfactants.
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Affiliation(s)
- Jie Zhang
- Department of Materials Science and Engineering, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Steve Granick
- IBS Center for Soft and Living Matter, UNIST , Ulsan 689-798, South Korea
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33
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Wang J, Gayatri MA, Ferguson AL. Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes. J Phys Chem B 2017; 121:4923-4944. [DOI: 10.1021/acs.jpcb.7b02574] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiang Wang
- Department
of Physics, University of Illinois Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Mohit A. Gayatri
- Department
of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department
of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Department
of Materials Science and Engineering, University of Illinois Urbana−Champaign, 1304 West Green Street, Urbana, Illinois 61801, United States
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34
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Patra TK, Meenakshisundaram V, Hung JH, Simmons DS. Neural-Network-Biased Genetic Algorithms for Materials Design: Evolutionary Algorithms That Learn. ACS COMBINATORIAL SCIENCE 2017; 19:96-107. [PMID: 27997791 DOI: 10.1021/acscombsci.6b00136] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Machine learning has the potential to dramatically accelerate high-throughput approaches to materials design, as demonstrated by successes in biomolecular design and hard materials design. However, in the search for new soft materials exhibiting properties and performance beyond those previously achieved, machine learning approaches are frequently limited by two shortcomings. First, because they are intrinsically interpolative, they are better suited to the optimization of properties within the known range of accessible behavior than to the discovery of new materials with extremal behavior. Second, they require large pre-existing data sets, which are frequently unavailable and prohibitively expensive to produce. Here we describe a new strategy, the neural-network-biased genetic algorithm (NBGA), for combining genetic algorithms, machine learning, and high-throughput computation or experiment to discover materials with extremal properties in the absence of pre-existing data. Within this strategy, predictions from a progressively constructed artificial neural network are employed to bias the evolution of a genetic algorithm, with fitness evaluations performed via direct simulation or experiment. In effect, this strategy gives the evolutionary algorithm the ability to "learn" and draw inferences from its experience to accelerate the evolutionary process. We test this algorithm against several standard optimization problems and polymer design problems and demonstrate that it matches and typically exceeds the efficiency and reproducibility of standard approaches including a direct-evaluation genetic algorithm and a neural-network-evaluated genetic algorithm. The success of this algorithm in a range of test problems indicates that the NBGA provides a robust strategy for employing informatics-accelerated high-throughput methods to accelerate materials design in the absence of pre-existing data.
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Affiliation(s)
- Tarak K. Patra
- Department of Polymer Engineering, The University of Akron, 250 South Forge Street, Akron, Ohio 44325, United States
| | - Venkatesh Meenakshisundaram
- Department of Polymer Engineering, The University of Akron, 250 South Forge Street, Akron, Ohio 44325, United States
| | - Jui-Hsiang Hung
- Department of Polymer Engineering, The University of Akron, 250 South Forge Street, Akron, Ohio 44325, United States
| | - David S. Simmons
- Department of Polymer Engineering, The University of Akron, 250 South Forge Street, Akron, Ohio 44325, United States
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35
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Cui J, Long D, Shapturenka P, Kretzschmar I, Chen X, Wang T. Janus particle-based microprobes: Determination of object orientation. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2016.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Long AW, Phillips CL, Jankowksi E, Ferguson AL. Nonlinear machine learning and design of reconfigurable digital colloids. SOFT MATTER 2016; 12:7119-7135. [PMID: 27498992 DOI: 10.1039/c6sm01156j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Digital colloids, a cluster of freely rotating "halo" particles tethered to the surface of a central particle, were recently proposed as ultra-high density memory elements for information storage. Rational design of these digital colloids for memory storage applications requires a quantitative understanding of the thermodynamic and kinetic stability of the configurational states within which information is stored. We apply nonlinear machine learning to Brownian dynamics simulations of these digital colloids to extract the low-dimensional intrinsic manifold governing digital colloid morphology, thermodynamics, and kinetics. By modulating the relative size ratio between halo particles and central particles, we investigate the size-dependent configurational stability and transition kinetics for the 2-state tetrahedral (N = 4) and 30-state octahedral (N = 6) digital colloids. We demonstrate the use of this framework to guide the rational design of a memory storage element to hold a block of text that trades off the competing design criteria of memory addressability and volatility.
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Affiliation(s)
- Andrew W Long
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Zhang J, Granick S. Natural selection in the colloid world: active chiral spirals. Faraday Discuss 2016; 191:35-46. [DOI: 10.1039/c6fd00077k] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a model system in which to study natural selection in the colloid world. In the assembly of active Janus particles into rotating pinwheels when mixed with trace amounts of homogeneous colloids in the presence of an AC electric field, broken symmetry in the rotation direction produces spiral, chiral shapes. Locked into a central rotation point by the centre particle, the spiral arms are found to trail rotation of the overall cluster. To achieve a steady state, the spiral arms undergo an evolutionary process to coordinate their motion. Because all the particles as segments of the pinwheel arms are self-propelled, asymmetric arm lengths are tolerated. Reconfiguration of these structures can happen in various ways and various mechanisms of this directed structural change are analyzed in detail. We introduce the concept of VIP (very important particles) to express that sustainability of active structures is most sensitive to only a few particles at strategic locations in the moving self-assembled structures.
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Affiliation(s)
- Jie Zhang
- Department of Materials Science and Engineering
- University of Illinois
- Urbana
- USA
| | - Steve Granick
- IBS Centre for Soft and Living Matter
- Department of Chemistry
- UNIST (Ulsan National Institute of Science and Technology)
- Ulsan 689-798
- South Korea
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