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Boiko DA, Arkhipova DM, Ananikov VP. Recognition of Molecular Structure of Phosphonium Salts from the Visual Appearance of Material with Deep Learning Can Reveal Subtle Homologs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2403423. [PMID: 39254289 DOI: 10.1002/smll.202403423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/31/2024] [Indexed: 09/11/2024]
Abstract
Determining molecular structures is foundational in chemistry and biology. The notion of discerning molecular structures simply from the visual appearance of a material remained almost unthinkable until the advent of machine learning. This paper introduces a pioneering approach bridging the visual appearance of materials (both at the micro- and nanostructural levels) with traditional chemical structure analysis methods. Quaternary phosphonium salts are opted as the model compounds, given their significant roles in diverse chemical and medicinal fields and their ability to form homologs with only minute intermolecular variances. This research results in the successful creation of a neural network model capable of recognizing molecular structures from visual electron microscopy images of the material. The performance of the model is evaluated and related to the chemical nature of the studied chemicals. Additionally, unsupervised domain transfer is tested as a method to use the resulting model on optical microscopy images, as well as test models trained on optical images directly. The robustness of the method is further tested using a complex system of phosphonium salt mixtures. To the best of the authors' knowledge, this study offers the first evidence of the feasibility of discerning nearly indistinguishable molecular structures.
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Affiliation(s)
- Daniil A Boiko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
| | - Daria M Arkhipova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
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Khare E, Gonzalez Obeso C, Martín-Moldes Z, Talib A, Kaplan DL, Holten-Andersen N, Blank KG, Buehler MJ. Heterogeneous and Cooperative Rupture of Histidine-Ni 2+ Metal-Coordination Bonds on Rationally Designed Protein Templates. ACS Biomater Sci Eng 2024; 10:2945-2955. [PMID: 38669114 DOI: 10.1021/acsbiomaterials.3c01819] [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] [Indexed: 04/28/2024]
Abstract
Metal-coordination bonds, a highly tunable class of dynamic noncovalent interactions, are pivotal to the function of a variety of protein-based natural materials and have emerged as binding motifs to produce strong, tough, and self-healing bioinspired materials. While natural proteins use clusters of metal-coordination bonds, synthetic materials frequently employ individual bonds, resulting in mechanically weak materials. To overcome this current limitation, we rationally designed a series of elastin-like polypeptide templates with the capability of forming an increasing number of intermolecular histidine-Ni2+ metal-coordination bonds. Using single-molecule force spectroscopy and steered molecular dynamics simulations, we show that templates with three histidine residues exhibit heterogeneous rupture pathways, including the simultaneous rupture of at least two bonds with more-than-additive rupture forces. The methodology and insights developed improve our understanding of the molecular interactions that stabilize metal-coordinated proteins and provide a general route for the design of new strong, metal-coordinated materials with a broad spectrum of dissipative time scales.
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Affiliation(s)
- Eesha Khare
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | | | - Zaira Martín-Moldes
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ayesha Talib
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Niels Holten-Andersen
- Department of Bioengineering and Materials Science and EngineeringLehigh University, 27 Memorial Dr W, Bethlehem, Pennsylvania 18015, United States
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
- Department of Biomolecular & Selforganizing Matter, Institute of Experimental Physics, Johannes Kepler University, Altenberger Strasse 69, 4040 Linz, Austria
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Shen SC, Lee NA, Lockett WJ, Acuil AD, Gazdus HB, Spitzer BN, Buehler MJ. Robust myco-composites: a biocomposite platform for versatile hybrid-living materials. MATERIALS HORIZONS 2024; 11:1689-1703. [PMID: 38315077 DOI: 10.1039/d3mh01277h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Fungal mycelium, a living network of filamentous threads, thrives on lignocellulosic waste and exhibits rapid growth, hydrophobicity, and intrinsic regeneration, offering a potential means to create next-generation sustainable and functional composites. However, existing hybrid-living mycelium composites (myco-composites) are tremendously constrained by conventional mold-based manufacturing processes, which are only compatible with simple geometries and coarse biomass substrates that enable gas exchange. Here we introduce a class of structural myco-composites manufactured with a novel platform that harnesses high-resolution biocomposite additive manufacturing and robust mycelium colonization with indirect inoculation. We leverage principles of hierarchical composite design and selective nutritional provision to create a robust myco-composite that is scalable, tunable, and compatible with complex geometries. To illustrate the versatility of this platform, we characterize the impact of mycelium colonization on mechanical and surface properties of the composite. We found that our method yields the strongest mycelium composite reported to date with a modulus of 160 MPa and tensile strength of 0.72 MPa, which represents over a 15-fold improvement over typical mycelium composites, and further demonstrate unique applications with fabrication of foldable bio-welded containers and flexible mycelium textiles. This study bridges the gap between biocomposite and hybrid-living materials research, opening the door to advanced structural mycelium applications and demonstrating a novel platform for development of diverse hybrid-living materials.
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Affiliation(s)
- Sabrina C Shen
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Nicolas A Lee
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- School of Architecture and Planning, Media Lab, Massachusetts Institute of Technology, 75 Amherst Street, Cambridge, MA, 02139, USA
| | - William J Lockett
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- MIT Center for Art, Science & Technology (CAST), Massachusetts Institute of Technology, 77 Massachusetts Ave. 10-183, Cambridge, MA 02139, USA
- Department of Media, Culture, and Communication, New York University, 239 Greene Street, New York, NY, 10003, USA
| | - Aliai D Acuil
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Hannah B Gazdus
- School of Architecture and Planning, Media Lab, Massachusetts Institute of Technology, 75 Amherst Street, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Branden N Spitzer
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave. 1-165, Cambridge, MA, 02139, USA.
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
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Deb J, Saikia L, Dihingia KD, Sastry GN. ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT. J Chem Inf Model 2024; 64:799-811. [PMID: 38237025 DOI: 10.1021/acs.jcim.3c01702] [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: 02/13/2024]
Abstract
The pursuit of designing smart and functional materials is of paramount importance across various domains, such as material science, engineering, chemical technology, electronics, biomedicine, energy, and numerous others. Consequently, researchers are actively involved in the development of innovative models and strategies for material design. Recent advancements in analytical tools, experimentation, and computer technology additionally enhance the material design possibilities. Notably, data-driven techniques like artificial intelligence and machine learning have achieved substantial progress in exploring various applications within material science. One such approach, ChatGPT, a large language model, holds transformative potential for addressing complex queries. In this article, we explore ChatGPT's understanding of material science by assigning some simple tasks across various subareas of computational material science. The findings indicate that while ChatGPT may make some minor errors in accomplishing general tasks, it demonstrates the capability to learn and adapt through human interactions. However, issues like output consistency, probable hidden errors, and ethical consequences should be addressed.
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Affiliation(s)
- Jyotirmoy Deb
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Lakshi Saikia
- Advanced Materials Group, Materials Sciences & Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Kripa Dristi Dihingia
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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Badini S, Regondi S, Pugliese R. Unleashing the Power of Artificial Intelligence in Materials Design. MATERIALS (BASEL, SWITZERLAND) 2023; 16:5927. [PMID: 37687620 PMCID: PMC10488647 DOI: 10.3390/ma16175927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
The integration of artificial intelligence (AI) algorithms in materials design is revolutionizing the field of materials engineering thanks to their power to predict material properties, design de novo materials with enhanced features, and discover new mechanisms beyond intuition. In addition, they can be used to infer complex design principles and identify high-quality candidates more rapidly than trial-and-error experimentation. From this perspective, herein we describe how these tools can enable the acceleration and enrichment of each stage of the discovery cycle of novel materials with optimized properties. We begin by outlining the state-of-the-art AI models in materials design, including machine learning (ML), deep learning, and materials informatics tools. These methodologies enable the extraction of meaningful information from vast amounts of data, enabling researchers to uncover complex correlations and patterns within material properties, structures, and compositions. Next, a comprehensive overview of AI-driven materials design is provided and its potential future prospects are highlighted. By leveraging such AI algorithms, researchers can efficiently search and analyze databases containing a wide range of material properties, enabling the identification of promising candidates for specific applications. This capability has profound implications across various industries, from drug development to energy storage, where materials performance is crucial. Ultimately, AI-based approaches are poised to revolutionize our understanding and design of materials, ushering in a new era of accelerated innovation and advancement.
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