1
|
Duke R, Yang CH, Ganapathysubramanian B, Risko C. Evaluating Molecular Similarity Measures: Do Similarity Measures Reflect Electronic Structure Properties? J Chem Inf Model 2025; 65:4311-4319. [PMID: 40299458 DOI: 10.1021/acs.jcim.5c00175] [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: 04/30/2025]
Abstract
The rapid adoption of big data, machine learning (ML), and generative artificial intelligence (AI) in chemical discovery has heightened the importance of quantifying molecular similarity. Molecular similarity, commonly assessed as the distance between molecular fingerprints, is integral to applications such as database curation, diversity analysis, and property prediction. AI tools frequently rely on these similarity measures to cluster molecules under the assumption that structurally similar molecules exhibit similar properties. However, this assumption is not universally valid, particularly for continuous properties like electronic structure properties. Despite the prevalence of fingerprint-based similarity measures, their evaluation has largely depended on biological activity data sets and qualitative metrics, limiting their relevance for nonbiological domains. To address this gap, we propose a framework to evaluate the correlation between molecular similarity measures and molecular properties. Our approach builds on the concept of neighborhood behavior and incorporates kernel density estimation (KDE) analysis to quantify how well similarity measures capture property relationships. Using a data set of over 350 million molecule pairs with electronic structure, redox, and optical properties, we systematically evaluate the correlation between several molecular fingerprint generators, distance functions, and these properties. Both the curated data set and the evaluation framework are publicly available.
Collapse
Affiliation(s)
- Rebekah Duke
- Department of Chemistry and Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Chih-Hsuan Yang
- Department of Mechanical Engineering and Translational AI Research and Education Center, Iowa State University, Ames, Iowa 50011, United States
| | - Baskar Ganapathysubramanian
- Department of Mechanical Engineering and Translational AI Research and Education Center, Iowa State University, Ames, Iowa 50011, United States
| | - Chad Risko
- Department of Chemistry and Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| |
Collapse
|
2
|
Zaki M, Prinz C, Ruehle B. A Self-Driving Lab for Nano- and Advanced Materials Synthesis. ACS NANO 2025; 19:9029-9041. [PMID: 39995288 PMCID: PMC11912568 DOI: 10.1021/acsnano.4c17504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 02/10/2025] [Accepted: 02/11/2025] [Indexed: 02/26/2025]
Abstract
The recent emergence of self-driving laboratories (SDL) and material acceleration platforms (MAPs) demonstrates the ability of these systems to change the way chemistry and material syntheses will be performed in the future. Especially in conjunction with nano- and advanced materials which are generally recognized for their great potential in solving current material science challenges, such systems can make disrupting contributions. Here, we describe in detail MINERVA, an SDL specifically built and designed for the synthesis, purification, and in line characterization of nano- and advanced materials. By fully automating these three process steps for seven different materials from five representative, completely different classes of nano- and advanced materials (metal, metal oxide, silica, metal organic framework, and core-shell particles) that follow different reaction mechanisms, we demonstrate the great versatility and flexibility of the platform. We further study the reproducibility and particle size distributions of these seven representative materials in depth and show the excellent performance of the platform when synthesizing these material classes. Lastly, we discuss the design considerations as well as the hardware and software components that went into building the platform and make all of the components publicly available.
Collapse
Affiliation(s)
- Mohammad Zaki
- Federal
Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse
11, D-12489 Berlin, Germany
- Humboldt
University Berlin, Unter
den Linden 6, D-10117 Berlin, Germany
| | - Carsten Prinz
- Federal
Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse
11, D-12489 Berlin, Germany
| | - Bastian Ruehle
- Federal
Institute for Materials Research and Testing (BAM), Richard-Willstätter-Strasse
11, D-12489 Berlin, Germany
| |
Collapse
|
3
|
Muroga S, Honda T, Miki Y, Nakajima H, Futaba DN, Hata K. Real-time autonomous control of a continuous macroscopic process as demonstrated by plastic forming. MATERIALS HORIZONS 2025; 12:623-629. [PMID: 39508391 DOI: 10.1039/d4mh00051j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
To meet the need for more adaptable and expedient approaches in research and manufacturing, we present a continuous autonomous system that leverages real-time, in situ characterization and an active-learning-based decision-making processor. This system was applied to a plastic film forming process to demonstrate its capability in autonomously determining process conditions for specified film dimensions without human intervention. Application of the system to nine film dimensions (width and thickness) highlighted its ability to explore the search space and identify appropriate and stable process conditions, with an average of 11 characterization-adjustment iterations and a processing time of 19 minutes per width, thickness combination. The system successfully avoided common pitfalls, such as repetitive over-correction, and demonstrated high accuracy, with R2 values of 0.87 and 0.90 for film width and thickness, respectively. Moreover, the active learning algorithm enabled the system to begin exploration with zero training data, effectively addressing the complex and interdependent relationships between control factors (material supply rate, applied force, material viscosity) in the continuous plastic forming process. Given that the core concept of this autonomous process can, in principle, be transferred to other continuous material processing systems, these results have implications for accelerating progress in both research and industry.
Collapse
Affiliation(s)
- Shun Muroga
- Nano Carbon Device Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Takashi Honda
- Research Association of High-Throughput Design and Development for Advanced Functional Materials (ADMAT), Tsukuba, Ibaraki, 305-8568, Japan
| | - Yasuaki Miki
- Nano Carbon Device Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Hideaki Nakajima
- Nano Carbon Device Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Don N Futaba
- Nano Carbon Device Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Kenji Hata
- Nano Carbon Device Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| |
Collapse
|
4
|
Foadian E, Sanchez S, Kalinin SV, Ahmadi M. From Sunlight to Solutions: Closing the Loop on Halide Perovskites. ACS MATERIALS AU 2025; 5:11-23. [PMID: 39802149 PMCID: PMC11718539 DOI: 10.1021/acsmaterialsau.4c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/20/2024] [Accepted: 10/21/2024] [Indexed: 01/16/2025]
Abstract
Halide perovskites (HPs) are emerging as key materials in the fight against global warming with well recognized applications, such as photovoltaics, and emergent opportunities, such as photocatalysis for methane removal and environmental remediation. These current and emergent applications are enabled by a unique combination of high absorption coefficients, tunable band gaps, and long carrier diffusion lengths, making them highly efficient for solar energy conversion. To address the challenge of discovery and optimization of HPs in huge chemical and compositional spaces of possible candidates, this perspective discusses a comprehensive strategy for screening HPs through automated high-throughput and combinatorial synthesis techniques. A critical aspect of this approach is closing the characterization loop, where machine learning (ML) and human collaboration play pivotal roles. By leveraging human creativity and domain knowledge for hypothesis generation and employing ML to test and refine these hypotheses efficiently, we aim to accelerate the discovery and optimization of HPs under specific environmental conditions. This synergy enables rapid identification of the most promising materials, advancing from fundamental discovery to scalable manufacturability. Our ultimate goal of this work is to transition from laboratory-scale innovations to real-world applications, ensuring that HPs can be deployed effectively in technologies that mitigate global warming, such as in solar energy harvesting and methane removal systems.
Collapse
Affiliation(s)
- Elham Foadian
- Institute
for Advanced Materials and Manufacturing, Department of Materials Science and Engineering, Knoxville, Tennessee 37996, United States
| | - Sheryl Sanchez
- Institute
for Advanced Materials and Manufacturing, Department of Materials Science and Engineering, Knoxville, Tennessee 37996, United States
| | - Sergei V. Kalinin
- Institute
for Advanced Materials and Manufacturing, Department of Materials Science and Engineering, Knoxville, Tennessee 37996, United States
- Physical
Science Directorate, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Mahshid Ahmadi
- Institute
for Advanced Materials and Manufacturing, Department of Materials Science and Engineering, Knoxville, Tennessee 37996, United States
| |
Collapse
|
5
|
Yoo HJ, Lee KY, Kim D, Han SS. OCTOPUS: operation control system for task optimization and job parallelization via a user-optimal scheduler. Nat Commun 2024; 15:9669. [PMID: 39516207 PMCID: PMC11549402 DOI: 10.1038/s41467-024-54067-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
The material acceleration platform, empowered by robotics and artificial intelligence, is a transformative approach for expediting material discovery processes across diverse domains. However, the development of an operating system for material acceleration platform faces challenges in simultaneously managing diverse experiments from multiple users. Specifically, when it is utilized by multiple users, the overlapping challenges of experimental modules or devices can lead to inefficiencies in both resource utilization and safety hazards. To overcome these challenges, we present an operation control system for material acceleration platform, namely, OCTOPUS, which is an acronym for operation control system for task optimization and job parallelization via a user-optimal scheduler. OCTOPUS streamlines experiment scheduling and optimizes resource utilization through integrating its interface node, master node and module nodes. Leveraging process modularization and a network protocol, OCTOPUS ensures the homogeneity, scalability, safety and versatility of the platform. In addition, OCTOPUS embodies a user-optimal scheduler. Job parallelization and task optimization techniques mitigate delays and safety hazards within realistic operational environments, while the closed-packing schedule algorithm efficiently executes multiple jobs with minimal resource waste. Copilot of OCTOPUS is developed to promote the reusability of OCTOPUS for potential users with their own sets of lab resources, which substantially simplifies the process of code generation and customization through GPT recommendations and client feedback. This work offers a solution to the challenges encountered within the platform accessed by multiple users, and thereby will facilitate its widespread adoption in material development processes.
Collapse
Affiliation(s)
- Hyuk Jun Yoo
- Computational Science Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
| | - Kwan-Young Lee
- Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea.
| | - Donghun Kim
- Computational Science Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea.
| | - Sang Soo Han
- Computational Science Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea.
| |
Collapse
|
6
|
Jing Y, Low AKY, Liu Y, Feng M, Lim JWM, Loh SM, Rehman Q, Blundel SA, Mathews N, Hippalgaonkar K, Sum TC, Bruno A, Mhaisalkar SG. Stable and Highly Emissive Infrared Yb-Doped Perovskite Quantum Cutters Engineered by Machine Learning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2405973. [PMID: 39081096 DOI: 10.1002/adma.202405973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/10/2024] [Indexed: 11/02/2024]
Abstract
Quantum cutting (QC) allows the conversion of high-energy photons into lower-energy photons, exhibiting great potential for infrared communications. Yb-doped perovskite nanocrystals can achieve an efficient QC process with extremely high photoluminescence quantum yield (PLQY) thanks to the favorable Yb3+ incorporation in the perovskite structure. However, conventionally used oleic acid-oleylamine-based ligand pairs cause instability issues due to highly dynamic binding to surface states that have curbed their potential applications. Herein, zwitterionic type C3-sulfobetaine 3-(N,N-Dimethylpalmitylammonio)propanesulfonate molecule is utilized to build a strong binding state on the nanocrystals' surface through a new phosphine oxide synthesis route. Leveraging machine learning and Bayesian Optimization workflow to determine optimal synthesis conditions, near-infrared PLQY above 190% is achieved. The high PLQY is well maintained after over three months of aging, under high-flux continuous UV irradiation, and long continuous annealing. This is the first report of highly efficient and stable perovskite quantum cutters, which will drive the study of fundamental physics phenomena and near-infrared quantum communications.
Collapse
Affiliation(s)
- Yao Jing
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Collaborative Initiative, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, 637335, Singapore
- Energy Research Institute @Nanyang Technological University (ERI@N), Research Techno Plaza, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Andre K Y Low
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Singapore
| | - Yun Liu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Singapore
| | - Minjun Feng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Jia Wei Melvin Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Siow Mean Loh
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble, F-38000, France
| | - Quadeer Rehman
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Steven A Blundel
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble, F-38000, France
| | - Nripan Mathews
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Energy Research Institute @Nanyang Technological University (ERI@N), Research Techno Plaza, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Kedar Hippalgaonkar
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Singapore
| | - Tze Chien Sum
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Annalisa Bruno
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Energy Research Institute @Nanyang Technological University (ERI@N), Research Techno Plaza, 50 Nanyang Drive, Singapore, 637553, Singapore
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Subodh G Mhaisalkar
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Energy Research Institute @Nanyang Technological University (ERI@N), Research Techno Plaza, 50 Nanyang Drive, Singapore, 637553, Singapore
- SKKU Institute of Energy Science and Technology (SIEST), Sungkyunkwan University, Seobu-ro, Jangan-gu, Suwon-si, Gyeonggi-do, 2066, South Korea
| |
Collapse
|
7
|
Falling LJ. A Vision for the Future of Materials Innovation and How to Fast-Track It with Services. ACS PHYSICAL CHEMISTRY AU 2024; 4:420-429. [PMID: 39346604 PMCID: PMC11428258 DOI: 10.1021/acsphyschemau.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 10/01/2024]
Abstract
Today, we witness how our scientific ecosystem tries to accommodate a new form of intelligence, artificial intelligence (AI). To make the most of AI in materials science, we need to make the data from computational and laboratory experiments machine-readable, but while that works well for computational experiments, integrating laboratory hardware into a digital workflow seems to be a formidable barrier toward that goal. This paper explores measurement services as a way to lower this barrier. I envision the Entity for Multivariate Material Analysis (EMMA), a centralized service that offers measurement bundles tailored for common research needs. EMMA's true strength, however, lies in its software ecosystem to treat, simulate, and store the measured data. Its close integration of measurements and their simulation not only produces metadata-rich experimental data but also provides a self-consistent framework that links the sample with a snapshot of its digital twin. If EMMA was to materialize, its database of experimental data connected to digital twins could serve as the fuel for physics-informed machine learning and a trustworthy horizon of expectations for material properties. This drives material innovation since knowing the statistics helps find the exceptional. This is the EMMA approach: fast-tracking material innovation by integrated measurement and software services.
Collapse
Affiliation(s)
- Lorenz J Falling
- School of Natural Sciences, Technical University Munich, 85748 Munich, Germany
| |
Collapse
|
8
|
Tom G, Schmid SP, Baird SG, Cao Y, Darvish K, Hao H, Lo S, Pablo-García S, Rajaonson EM, Skreta M, Yoshikawa N, Corapi S, Akkoc GD, Strieth-Kalthoff F, Seifrid M, Aspuru-Guzik A. Self-Driving Laboratories for Chemistry and Materials Science. Chem Rev 2024; 124:9633-9732. [PMID: 39137296 PMCID: PMC11363023 DOI: 10.1021/acs.chemrev.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Self-driving laboratories (SDLs) promise an accelerated application of the scientific method. Through the automation of experimental workflows, along with autonomous experimental planning, SDLs hold the potential to greatly accelerate research in chemistry and materials discovery. This review provides an in-depth analysis of the state-of-the-art in SDL technology, its applications across various scientific disciplines, and the potential implications for research and industry. This review additionally provides an overview of the enabling technologies for SDLs, including their hardware, software, and integration with laboratory infrastructure. Most importantly, this review explores the diverse range of scientific domains where SDLs have made significant contributions, from drug discovery and materials science to genomics and chemistry. We provide a comprehensive review of existing real-world examples of SDLs, their different levels of automation, and the challenges and limitations associated with each domain.
Collapse
Affiliation(s)
- Gary Tom
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Stefan P. Schmid
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 1, CH-8093 Zurich, Switzerland
| | - Sterling G. Baird
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Yang Cao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Kourosh Darvish
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Han Hao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Stanley Lo
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Sergio Pablo-García
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
| | - Ella M. Rajaonson
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Marta Skreta
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Naruki Yoshikawa
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Samantha Corapi
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Gun Deniz Akkoc
- Forschungszentrum
Jülich GmbH, Helmholtz Institute
for Renewable Energy Erlangen-Nürnberg, Cauerstr. 1, 91058 Erlangen, Germany
- Department
of Chemical and Biological Engineering, Friedrich-Alexander Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany
| | - Felix Strieth-Kalthoff
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- School of
Mathematics and Natural Sciences, University
of Wuppertal, Gaußstraße
20, 42119 Wuppertal, Germany
| | - Martin Seifrid
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States of America
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
- Department
of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department
of Materials Science & Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
- Lebovic
Fellow, Canadian Institute for Advanced
Research (CIFAR), 661
University Ave, Toronto, Ontario M5G 1M1, Canada
| |
Collapse
|
9
|
Johnson NS, Mishra AA, Kirsch DJ, Mehta A. Active Learning for Rapid Targeted Synthesis of Compositionally Complex Alloys. MATERIALS (BASEL, SWITZERLAND) 2024; 17:4038. [PMID: 39203216 PMCID: PMC11355945 DOI: 10.3390/ma17164038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/03/2024] [Accepted: 08/06/2024] [Indexed: 09/03/2024]
Abstract
The next generation of advanced materials is tending toward increasingly complex compositions. Synthesizing precise composition is time-consuming and becomes exponentially demanding with increasing compositional complexity. An experienced human operator does significantly better than a novice but still struggles to consistently achieve precision when synthesis parameters are coupled. The time to optimize synthesis becomes a barrier to exploring scientifically and technologically exciting compositionally complex materials. This investigation demonstrates an active learning (AL) approach for optimizing physical vapor deposition synthesis of thin-film alloys with up to five principal elements. We compared AL-based on Gaussian process (GP) and random forest (RF) models. The best performing models were able to discover synthesis parameters for a target quinary alloy in 14 iterations. We also demonstrate the capability of these models to be used in transfer learning tasks. RF and GP models trained on lower dimensional systems (i.e., ternary, quarternary) show an immediate improvement in prediction accuracy compared to models trained only on quinary samples. Furthermore, samples that only share a few elements in common with the target composition can be used for model pre-training. We believe that such AL approaches can be widely adapted to significantly accelerate the exploration of compositionally complex materials.
Collapse
Affiliation(s)
- Nathan S. Johnson
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; (A.A.M.); (A.M.)
| | | | - Dylan J. Kirsch
- Materials Science and Engineering Department, University of Maryland, College Park, MD 20742, USA;
| | - Apurva Mehta
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; (A.A.M.); (A.M.)
| |
Collapse
|
10
|
Suvarna M, Zou T, Chong SH, Ge Y, Martín AJ, Pérez-Ramírez J. Active learning streamlines development of high performance catalysts for higher alcohol synthesis. Nat Commun 2024; 15:5844. [PMID: 38992019 PMCID: PMC11239856 DOI: 10.1038/s41467-024-50215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Developing efficient catalysts for syngas-based higher alcohol synthesis (HAS) remains a formidable research challenge. The chain growth and CO insertion requirements demand multicomponent materials, whose complex reaction dynamics and extensive chemical space defy catalyst design norms. We present an alternative strategy by integrating active learning into experimental workflows, exemplified via the FeCoCuZr catalyst family. Our data-aided framework streamlines navigation of the extensive composition and reaction condition space in 86 experiments, offering >90% reduction in environmental footprint and costs over traditional programs. It identifies the Fe65Co19Cu5Zr11 catalyst with optimized reaction conditions to attain higher alcohol productivities of 1.1 gHA h-1 gcat-1 under stable operation for 150 h on stream, a 5-fold improvement over typically reported yields. Characterization reveals catalytic properties linked to superior activities despite moderate higher alcohol selectivities. To better reflect catalyst demands, we devise multi-objective optimization to maximize higher alcohol productivity while minimizing undesired CO2 and CH4 selectivities. An intrinsic trade-off between these metrics is uncovered, identifying Pareto-optimal catalysts not readily discernible by human experts. Finally, based on feature-importance analysis, we formulate data-informed guidelines to develop performance-specific FeCoCuZr systems. This approach goes beyond existing HAS catalyst design strategies, is adaptable to broader catalytic transformations, and fosters laboratory sustainability.
Collapse
Affiliation(s)
- Manu Suvarna
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Tangsheng Zou
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Sok Ho Chong
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Yuzhen Ge
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Antonio J Martín
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Javier Pérez-Ramírez
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland.
| |
Collapse
|
11
|
Bao Z, Yung F, Hickman RJ, Aspuru-Guzik A, Bannigan P, Allen C. Data-driven development of an oral lipid-based nanoparticle formulation of a hydrophobic drug. Drug Deliv Transl Res 2024; 14:1872-1887. [PMID: 38158474 DOI: 10.1007/s13346-023-01491-9] [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] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Due to its cost-effectiveness, convenience, and high patient adherence, oral drug administration normally remains the preferred approach. Yet, the effective delivery of hydrophobic drugs via the oral route is often hindered by their limited water solubility and first-pass metabolism. To mitigate these challenges, advanced delivery systems such as solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) have been developed to encapsulate hydrophobic drugs and enhance their bioavailability. However, traditional design methodologies for these complex formulations often present intricate challenges because they are restricted to a relatively narrow design space. Here, we present a data-driven approach for the accelerated design of SLNs/NLCs encapsulating a model hydrophobic drug, cannabidiol, that combines experimental automation and machine learning. A small subset of formulations, comprising 10% of all formulations in the design space, was prepared in-house, leveraging miniaturized experimental automation to improve throughput and decrease the quantity of drug and materials required. Machine learning models were then trained on the data generated from these formulations and used to predict properties of all SLNs/NLCs within this design space (i.e., 1215 formulations). Notably, formulations predicted to be high-performers via this approach were confirmed to significantly enhance the solubility of the drug by up to 3000-fold and prevented degradation of drug. Moreover, the high-performance formulations significantly enhanced the oral bioavailability of the drug compared to both its free form and an over-the-counter version. Furthermore, this bioavailability matched that of a formulation equivalent in composition to the FDA-approved product, Epidiolex®.
Collapse
Affiliation(s)
- Zeqing Bao
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Fion Yung
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Riley J Hickman
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 2E4, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, M5S 1M1, Canada
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 2E4, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, M5S 1M1, Canada
- Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, M5S 1M1, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
- Department of Materials Science & Engineering, University of Toronto, Toronto, ON, M5S 3E4, Canada
- CIFAR Artificial Intelligence Research Chair, Vector Institute, Toronto, ON, M5S 1M1, Canada
- Acceleration Consortium, Toronto, ON, M5S 3H6, Canada
| | - Pauric Bannigan
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada.
| | - Christine Allen
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada.
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada.
- Acceleration Consortium, Toronto, ON, M5S 3H6, Canada.
| |
Collapse
|
12
|
Strohmann T, Melching D, Paysan F, Dietrich E, Requena G, Breitbarth E. Next generation fatigue crack growth experiments of aerospace materials. Sci Rep 2024; 14:14075. [PMID: 38890320 PMCID: PMC11189514 DOI: 10.1038/s41598-024-63915-x] [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: 09/07/2023] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
Today's societal challenges require rapid response and smart materials solutions in almost all technical areas. Driven by these needs, data-driven research has emerged as an enabler for faster innovation cycles. In fields such as chemistry, materials science and life sciences, automatic and even autonomous data generation and processing is already accelerating knowledge discovery. In contrast, in experimental mechanics, complex investigations like studying fatigue crack growth in structural materials have traditionally adhered to standardized procedures with limited adoption of the digital transformation. In this work, we present a novel infrastructure for data-centric experimental mechanics in the field of fatigue crack growth. Our methodology incorporates a robust code base that complements a multi-scale digital image correlation and robot-assisted test rig. Using this approach, the information-to-cost ratio of fatigue crack growth experiments in aerospace materials is significantly higher compared to traditional experiments. Thus, serves as a catalyst for discovering new scientific knowledge in the field of structural materials and structures.
Collapse
Affiliation(s)
- Tobias Strohmann
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany
| | - David Melching
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany
| | - Florian Paysan
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany
| | - Eric Dietrich
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany
| | - Guillermo Requena
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany
- Metallic Structures and Materials Systems for Aerospace Engineering, RWTH Aachen University, 52062, Aachen, Germany
| | - Eric Breitbarth
- German Aerospace Center (DLR), Institute of Materials Research, Linder Hoehe, 51147, Cologne, Germany.
| |
Collapse
|
13
|
Siemenn AE, Aissi E, Sheng F, Tiihonen A, Kavak H, Das B, Buonassisi T. Using scalable computer vision to automate high-throughput semiconductor characterization. Nat Commun 2024; 15:4654. [PMID: 38862468 PMCID: PMC11166656 DOI: 10.1038/s41467-024-48768-2] [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: 10/13/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
High-throughput materials synthesis methods, crucial for discovering novel functional materials, face a bottleneck in property characterization. These high-throughput synthesis tools produce 104 samples per hour using ink-based deposition while most characterization methods are either slow (conventional rates of 101 samples per hour) or rigid (e.g., designed for standard thin films), resulting in a bottleneck. To address this, we propose automated characterization (autocharacterization) tools that leverage adaptive computer vision for an 85x faster throughput compared to non-automated workflows. Our tools include a generalizable composition mapping tool and two scalable autocharacterization algorithms that: (1) autonomously compute the band gaps of 200 compositions in 6 minutes, and (2) autonomously compute the environmental stability of 200 compositions in 20 minutes, achieving 98.5% and 96.9% accuracy, respectively, when benchmarked against domain expert manual evaluation. These tools, demonstrated on the formamidinium (FA) and methylammonium (MA) mixed-cation perovskite system FA1-xMAxPbI3, 0 ≤ x ≤ 1, significantly accelerate the characterization process, synchronizing it closer to the rate of high-throughput synthesis.
Collapse
Affiliation(s)
- Alexander E Siemenn
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA.
| | - Eunice Aissi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA.
| | - Fang Sheng
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Armi Tiihonen
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
- Department of Applied Physics, Aalto University, Otakaari 24, Espoo, 02150, Finland
| | - Hamide Kavak
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
- Department of Physics, Cukurova University, Adana, 01330, Turkey
| | - Basita Das
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Tonio Buonassisi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| |
Collapse
|
14
|
Shrestha S, Barvenik KJ, Chen T, Yang H, Li Y, Kesavan MM, Little JM, Whitley HC, Teng Z, Luo Y, Tubaldi E, Chen PY. Machine intelligence accelerated design of conductive MXene aerogels with programmable properties. Nat Commun 2024; 15:4685. [PMID: 38824129 PMCID: PMC11144242 DOI: 10.1038/s41467-024-49011-8] [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: 09/23/2023] [Accepted: 05/14/2024] [Indexed: 06/03/2024] Open
Abstract
Designing ultralight conductive aerogels with tailored electrical and mechanical properties is critical for various applications. Conventional approaches rely on iterative, time-consuming experiments across a vast parameter space. Herein, an integrated workflow is developed to combine collaborative robotics with machine learning to accelerate the design of conductive aerogels with programmable properties. An automated pipetting robot is operated to prepare 264 mixtures of Ti3C2Tx MXene, cellulose, gelatin, and glutaraldehyde at different ratios/loadings. After freeze-drying, the aerogels' structural integrity is evaluated to train a support vector machine classifier. Through 8 active learning cycles with data augmentation, 162 unique conductive aerogels are fabricated/characterized via robotics-automated platforms, enabling the construction of an artificial neural network prediction model. The prediction model conducts two-way design tasks: (1) predicting the aerogels' physicochemical properties from fabrication parameters and (2) automating the inverse design of aerogels for specific property requirements. The combined use of model interpretation and finite element simulations validates a pronounced correlation between aerogel density and compressive strength. The model-suggested aerogels with high conductivity, customized strength, and pressure insensitivity allow for compression-stable Joule heating for wearable thermal management.
Collapse
Affiliation(s)
- Snehi Shrestha
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Kieran James Barvenik
- Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Tianle Chen
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Haochen Yang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yang Li
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Meera Muthachi Kesavan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Joshua M Little
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Hayden C Whitley
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Zi Teng
- US Department of Agriculture, Agricultural Research Service, Food Quality Laboratory and Environment Microbial Food Safety Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, 20725, USA
| | - Yaguang Luo
- US Department of Agriculture, Agricultural Research Service, Food Quality Laboratory and Environment Microbial Food Safety Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, 20725, USA
| | - Eleonora Tubaldi
- Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA.
- Maryland Robotics Center, College Park, MD, 20742, USA.
| | - Po-Yen Chen
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, 20742, USA.
- Maryland Robotics Center, College Park, MD, 20742, USA.
| |
Collapse
|
15
|
Chen T, Pang Z, He S, Li Y, Shrestha S, Little JM, Yang H, Chung TC, Sun J, Whitley HC, Lee IC, Woehl TJ, Li T, Hu L, Chen PY. Machine intelligence-accelerated discovery of all-natural plastic substitutes. NATURE NANOTECHNOLOGY 2024; 19:782-791. [PMID: 38499859 PMCID: PMC11186784 DOI: 10.1038/s41565-024-01635-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
One possible solution against the accumulation of petrochemical plastics in natural environments is to develop biodegradable plastic substitutes using natural components. However, discovering all-natural alternatives that meet specific properties, such as optical transparency, fire retardancy and mechanical resilience, which have made petrochemical plastics successful, remains challenging. Current approaches still rely on iterative optimization experiments. Here we show an integrated workflow that combines robotics and machine learning to accelerate the discovery of all-natural plastic substitutes with programmable optical, thermal and mechanical properties. First, an automated pipetting robot is commanded to prepare 286 nanocomposite films with various properties to train a support-vector machine classifier. Next, through 14 active learning loops with data augmentation, 135 all-natural nanocomposites are fabricated stagewise, establishing an artificial neural network prediction model. We demonstrate that the prediction model can conduct a two-way design task: (1) predicting the physicochemical properties of an all-natural nanocomposite from its composition and (2) automating the inverse design of biodegradable plastic substitutes that fulfils various user-specific requirements. By harnessing the model's prediction capabilities, we prepare several all-natural substitutes, that could replace non-biodegradable counterparts as exhibiting analogous properties. Our methodology integrates robot-assisted experiments, machine intelligence and simulation tools to accelerate the discovery and design of eco-friendly plastic substitutes starting from building blocks taken from the generally-recognized-as-safe database.
Collapse
Affiliation(s)
- Tianle Chen
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Zhenqian Pang
- Department of Mechanical Engineering, University of Maryland, College Park, MD, USA
| | - Shuaiming He
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Yang Li
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Snehi Shrestha
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Joshua M Little
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Haochen Yang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Tsai-Chun Chung
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Jiayue Sun
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - I-Chi Lee
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Taylor J Woehl
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Teng Li
- Department of Mechanical Engineering, University of Maryland, College Park, MD, USA.
| | - Liangbing Hu
- Department of Materials Science and Engineering, University of Maryland, College Park, MD, USA.
| | - Po-Yen Chen
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA.
- Maryland Robotics Center, College Park, MD, USA.
| |
Collapse
|
16
|
Ai Z, Zhang L, Chen Y, Long Y, Li B, Dong Q, Wang Y, Jiang J. On-Demand Optimization of Colorimetric Gas Sensors Using a Knowledge-Aware Algorithm-Driven Robotic Experimental Platform. ACS Sens 2024; 9:745-752. [PMID: 38331733 DOI: 10.1021/acssensors.3c02043] [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] [Indexed: 02/10/2024]
Abstract
Synthesizing the best material globally is challenging; it needs to know what and how much the best ingredient composition should be for satisfying multiple figures of merit simultaneously. Traditional one-variable-at-a-time methods are inefficient; the design-build-test-learn (DBTL) method could achieve the optimal composition from only a handful of ingredients. A vast design space needs to be explored to discover the possible global optimal composition for on-demand materials synthesis. This research developed a hypothesis-guided DBTL (H-DBTL) method combined with robots to expand the dimensions of the search space, thereby achieving a better global optimal performance. First, this study engineered the search space with knowledge-aware chemical descriptors and customized multiobjective functions to fulfill on-demand research objectives. To verify this concept, this novel method was used to optimize colorimetric ammonia sensors across a vast design space of as high as 19 variables, achieving two remarkable optimization goals within 1 week: first, a sensing array was developed for ammonia quantification of a wide dynamic range, from 0.5 to 500 ppm; second, a new state-of-the-art detection limit of 50 ppb was reached. This work demonstrates that the H-DBTL approach, combined with a robot, develops a novel paradigm for the on-demand optimization of functional materials.
Collapse
Affiliation(s)
- Zhehong Ai
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Longhan Zhang
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Yangguan Chen
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Yifan Long
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| | - Boyuan Li
- Hong Kong Center for Construction Robotics Limited, Hong Kong 808-815, China
| | - Qingyu Dong
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
- Polytechnic Institute, Zhejiang University, Hangzhou, Zhejiang 310015, China
| | - Yueming Wang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Space Active Optoelectronics Technology, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Jing Jiang
- Zhejiang Laboratory, Hangzhou, Zhejiang 311121, China
| |
Collapse
|
17
|
An Y, Webb MA, Jacobs WM. Active learning of the thermodynamics-dynamics trade-off in protein condensates. SCIENCE ADVANCES 2024; 10:eadj2448. [PMID: 38181073 PMCID: PMC10775998 DOI: 10.1126/sciadv.adj2448] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
Phase-separated biomolecular condensates exhibit a wide range of dynamic properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing the thermodynamic properties that govern phase separation. Using coarse-grained simulations of intrinsically disordered proteins, we show that the dynamics and thermodynamics of homopolymer condensates are strongly correlated, with increased condensate stability being coincident with low mobilities and high viscosities. We then apply an "active learning" strategy to identify heteropolymer sequences that break this correlation. This data-driven approach and accompanying analysis reveal how heterogeneous amino acid compositions and nonuniform sequence patterning map to a range of independently tunable dynamic and thermodynamic properties of biomolecular condensates. Our results highlight key molecular determinants governing the physical properties of biomolecular condensates and establish design rules for the development of stimuli-responsive biomaterials.
Collapse
Affiliation(s)
- Yaxin An
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - William M. Jacobs
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
18
|
Bai Y, Khoo ZHJ, I Made R, Xie H, Lim CYJ, Handoko AD, Chellappan V, Cheng JJ, Wei F, Lim YF, Hippalgaonkar K. Closed-Loop Multi-Objective Optimization for Cu-Sb-S Photo-Electrocatalytic Materials' Discovery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304269. [PMID: 37690005 DOI: 10.1002/adma.202304269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/17/2023] [Indexed: 09/11/2023]
Abstract
Copper antimony sulfides are regarded as promising catalysts for photo-electrochemical water splitting because of their earth abundance and broad light absorption. The unique photoactivity of copper antimony sulfides is dependent on their various crystalline structures and atomic compositions. Here, a closed-loop workflow is built, which explores Cu-Sb-S compositional space to optimize its photo-electrocatalytic hydrogen evolution from water, by integrating a high-throughput robotic platform, characterization techniques, and machine learning (ML) optimization workflow. The multi-objective optimization model discovers optimum experimental conditions after only nine cycles of integrated experiments-machine learning loop. Photocurrent testing at 0 V versus reversible hydrogen electrode (RHE) confirms the expected correlation between the materials' properties and photocurrent. An optimum photocurrent of -186 µA cm-2 is observed on Cu-Sb-S in the ratio of 9:45:46 in the form of single-layer coating on F-doped SnO2 (FTO) glass with a corresponding bandgap of 1.85 eV and 63.2% Cu1+ /Cu species content. The targeted intelligent search reveals a nonobvious CuSbS composition that exhibits 2.3 times greater activity than baseline results from random sampling.
Collapse
Affiliation(s)
- Yang Bai
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Zi Hui Jonathan Khoo
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore
| | - Riko I Made
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Huiqing Xie
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Carina Yi Jing Lim
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Albertus Denny Handoko
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore
| | - Vijila Chellappan
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Jianwei Jayce Cheng
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Fengxia Wei
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
| | - Yee-Fun Lim
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore, 627833, Republic of Singapore
| | - Kedar Hippalgaonkar
- Institute of Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore, 138634, Republic of Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Republic of Singapore
| |
Collapse
|
19
|
Kouba P, Kohout P, Haddadi F, Bushuiev A, Samusevich R, Sedlar J, Damborsky J, Pluskal T, Sivic J, Mazurenko S. Machine Learning-Guided Protein Engineering. ACS Catal 2023; 13:13863-13895. [PMID: 37942269 PMCID: PMC10629210 DOI: 10.1021/acscatal.3c02743] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Indexed: 11/10/2023]
Abstract
Recent progress in engineering highly promising biocatalysts has increasingly involved machine learning methods. These methods leverage existing experimental and simulation data to aid in the discovery and annotation of promising enzymes, as well as in suggesting beneficial mutations for improving known targets. The field of machine learning for protein engineering is gathering steam, driven by recent success stories and notable progress in other areas. It already encompasses ambitious tasks such as understanding and predicting protein structure and function, catalytic efficiency, enantioselectivity, protein dynamics, stability, solubility, aggregation, and more. Nonetheless, the field is still evolving, with many challenges to overcome and questions to address. In this Perspective, we provide an overview of ongoing trends in this domain, highlight recent case studies, and examine the current limitations of machine learning-based methods. We emphasize the crucial importance of thorough experimental validation of emerging models before their use for rational protein design. We present our opinions on the fundamental problems and outline the potential directions for future research.
Collapse
Affiliation(s)
- Petr Kouba
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
- Czech Institute
of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, 160 00 Prague 6, Czech Republic
- Faculty of
Electrical Engineering, Czech Technical
University in Prague, Technicka 2, 166 27 Prague 6, Czech Republic
| | - Pavel Kohout
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Faraneh Haddadi
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Anton Bushuiev
- Czech Institute
of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, 160 00 Prague 6, Czech Republic
| | - Raman Samusevich
- Czech Institute
of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, 160 00 Prague 6, Czech Republic
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Jiri Sedlar
- Czech Institute
of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, 160 00 Prague 6, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Tomas Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Josef Sivic
- Czech Institute
of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslavskych partyzanu 1580/3, 160 00 Prague 6, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| |
Collapse
|
20
|
Schrier J, Norquist AJ, Buonassisi T, Brgoch J. In Pursuit of the Exceptional: Research Directions for Machine Learning in Chemical and Materials Science. J Am Chem Soc 2023; 145:21699-21716. [PMID: 37754929 DOI: 10.1021/jacs.3c04783] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Exceptional molecules and materials with one or more extraordinary properties are both technologically valuable and fundamentally interesting, because they often involve new physical phenomena or new compositions that defy expectations. Historically, exceptionality has been achieved through serendipity, but recently, machine learning (ML) and automated experimentation have been widely proposed to accelerate target identification and synthesis planning. In this Perspective, we argue that the data-driven methods commonly used today are well-suited for optimization but not for the realization of new exceptional materials or molecules. Finding such outliers should be possible using ML, but only by shifting away from using traditional ML approaches that tweak the composition, crystal structure, or reaction pathway. We highlight case studies of high-Tc oxide superconductors and superhard materials to demonstrate the challenges of ML-guided discovery and discuss the limitations of automation for this task. We then provide six recommendations for the development of ML methods capable of exceptional materials discovery: (i) Avoid the tyranny of the middle and focus on extrema; (ii) When data are limited, qualitative predictions that provide direction are more valuable than interpolative accuracy; (iii) Sample what can be made and how to make it and defer optimization; (iv) Create room (and look) for the unexpected while pursuing your goal; (v) Try to fill-in-the-blanks of input and output space; (vi) Do not confuse human understanding with model interpretability. We conclude with a description of how these recommendations can be integrated into automated discovery workflows, which should enable the discovery of exceptional molecules and materials.
Collapse
Affiliation(s)
- Joshua Schrier
- Department of Chemistry, Fordham University, The Bronx, New York 10458, United States
| | - Alexander J Norquist
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, United States
| | - Tonio Buonassisi
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jakoah Brgoch
- Department of Chemistry and Texas Center for Superconductivity, University of Houston, Houston, Texas 77204, United States
| |
Collapse
|
21
|
Martin TB, Audus DJ. Emerging Trends in Machine Learning: A Polymer Perspective. ACS POLYMERS AU 2023; 3:239-258. [PMID: 37334191 PMCID: PMC10273415 DOI: 10.1021/acspolymersau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
In the last five years, there has been tremendous growth in machine learning and artificial intelligence as applied to polymer science. Here, we highlight the unique challenges presented by polymers and how the field is addressing them. We focus on emerging trends with an emphasis on topics that have received less attention in the review literature. Finally, we provide an outlook for the field, outline important growth areas in machine learning and artificial intelligence for polymer science and discuss important advances from the greater material science community.
Collapse
Affiliation(s)
- Tyler B. Martin
- National Institute of Standards
and Technology, Gaithersburg, Maryland20899, United States
| | - Debra J. Audus
- National Institute of Standards
and Technology, Gaithersburg, Maryland20899, United States
| |
Collapse
|
22
|
Anstine D, Isayev O. Generative Models as an Emerging Paradigm in the Chemical Sciences. J Am Chem Soc 2023; 145:8736-8750. [PMID: 37052978 PMCID: PMC10141264 DOI: 10.1021/jacs.2c13467] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/14/2023]
Abstract
Traditional computational approaches to design chemical species are limited by the need to compute properties for a vast number of candidates, e.g., by discriminative modeling. Therefore, inverse design methods aim to start from the desired property and optimize a corresponding chemical structure. From a machine learning viewpoint, the inverse design problem can be addressed through so-called generative modeling. Mathematically, discriminative models are defined by learning the probability distribution function of properties given the molecular or material structure. In contrast, a generative model seeks to exploit the joint probability of a chemical species with target characteristics. The overarching idea of generative modeling is to implement a system that produces novel compounds that are expected to have a desired set of chemical features, effectively sidestepping issues found in the forward design process. In this contribution, we overview and critically analyze popular generative algorithms like generative adversarial networks, variational autoencoders, flow, and diffusion models. We highlight key differences between each of the models, provide insights into recent success stories, and discuss outstanding challenges for realizing generative modeling discovered solutions in chemical applications.
Collapse
Affiliation(s)
- Dylan
M. Anstine
- Department
of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Olexandr Isayev
- Department
of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
23
|
Volk AA, Epps RW, Yonemoto DT, Masters BS, Castellano FN, Reyes KG, Abolhasani M. AlphaFlow: autonomous discovery and optimization of multi-step chemistry using a self-driven fluidic lab guided by reinforcement learning. Nat Commun 2023; 14:1403. [PMID: 36918561 PMCID: PMC10015005 DOI: 10.1038/s41467-023-37139-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Closed-loop, autonomous experimentation enables accelerated and material-efficient exploration of large reaction spaces without the need for user intervention. However, autonomous exploration of advanced materials with complex, multi-step processes and data sparse environments remains a challenge. In this work, we present AlphaFlow, a self-driven fluidic lab capable of autonomous discovery of complex multi-step chemistries. AlphaFlow uses reinforcement learning integrated with a modular microdroplet reactor capable of performing reaction steps with variable sequence, phase separation, washing, and continuous in-situ spectral monitoring. To demonstrate the power of reinforcement learning toward high dimensionality multi-step chemistries, we use AlphaFlow to discover and optimize synthetic routes for shell-growth of core-shell semiconductor nanoparticles, inspired by colloidal atomic layer deposition (cALD). Without prior knowledge of conventional cALD parameters, AlphaFlow successfully identified and optimized a novel multi-step reaction route, with up to 40 parameters, that outperformed conventional sequences. Through this work, we demonstrate the capabilities of closed-loop, reinforcement learning-guided systems in exploring and solving challenges in multi-step nanoparticle syntheses, while relying solely on in-house generated data from a miniaturized microfluidic platform. Further application of AlphaFlow in multi-step chemistries beyond cALD can lead to accelerated fundamental knowledge generation as well as synthetic route discoveries and optimization.
Collapse
Affiliation(s)
- Amanda A Volk
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695-7905, USA
| | - Robert W Epps
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695-7905, USA
| | - Daniel T Yonemoto
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Benjamin S Masters
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Felix N Castellano
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Kristofer G Reyes
- Department of Materials Design and Innovation, University at Buffalo, Buffalo, NY, 14260, USA
| | - Milad Abolhasani
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695-7905, USA.
| |
Collapse
|
24
|
Peng X, Wang X. Next-generation intelligent laboratories for materials design and manufacturing. MRS BULLETIN 2023; 48:179-185. [PMID: 36960275 PMCID: PMC9970134 DOI: 10.1557/s43577-023-00481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The contradiction between the importance of materials to modern society and their slow development process has led to the development of multiple methods to accelerate materials discovery. The recently emerged concept of intelligent laboratories integrates the developments in fields of high-throughput experimentation, automation, theoretical computing, and artificial intelligence to form a system that can autonomously carry out designed experiments and make scientific discoveries. We present the basic concepts and the foundations of this new research paradigm, demonstrate its typical application scenarios through case studies, and envision a collaborative human-machine meta laboratory in the future.
Collapse
Affiliation(s)
- Xiting Peng
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Xiaonan Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Laboratory of Industrial Biocatalysis (Tsinghua University), Ministry of Education, Beijing, China
| |
Collapse
|
25
|
Martin HG, Radivojevic T, Zucker J, Bouchard K, Sustarich J, Peisert S, Arnold D, Hillson N, Babnigg G, Marti JM, Mungall CJ, Beckham GT, Waldburger L, Carothers J, Sundaram S, Agarwal D, Simmons BA, Backman T, Banerjee D, Tanjore D, Ramakrishnan L, Singh A. Perspectives for self-driving labs in synthetic biology. Curr Opin Biotechnol 2023; 79:102881. [PMID: 36603501 DOI: 10.1016/j.copbio.2022.102881] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior. However, the level of investment required for the creation of biological SDLs is only warranted if directed toward solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.
Collapse
Affiliation(s)
- Hector G Martin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; BCAM, Basque Center for Applied Mathematics, Bilbao, Spain.
| | - Tijana Radivojevic
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Jeremy Zucker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA, United States
| | - Kristofer Bouchard
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, Berkeley, CA, United States
| | - Jess Sustarich
- Joint BioEnergy Institute, Emeryville, CA, United States; Biomaterials and Biomanufacturing Division, Sandia National Laboratories, Livermore, CA, United States
| | - Sean Peisert
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; University of California, Davis, Department of Computer Science, Davis, CA, United States
| | - Dan Arnold
- Lawrence Berkeley National Laboratory, Energy Storage and Distributed Resources Division, Berkeley, CA, United States
| | - Nathan Hillson
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Gyorgy Babnigg
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jose M Marti
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Christopher J Mungall
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Lucas Waldburger
- Department of Bioengineering, University of California, Berkeley, CA, United States
| | - James Carothers
- Department of Chemical Engineering, Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA, United States
| | - ShivShankar Sundaram
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States; Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Deb Agarwal
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Blake A Simmons
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Tyler Backman
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepanwita Banerjee
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepti Tanjore
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lavanya Ramakrishnan
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Anup Singh
- Joint BioEnergy Institute, Emeryville, CA, United States; Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| |
Collapse
|
26
|
Autonomous optimization of non-aqueous Li-ion battery electrolytes via robotic experimentation and machine learning coupling. Nat Commun 2022; 13:5454. [PMID: 36167832 PMCID: PMC9515088 DOI: 10.1038/s41467-022-32938-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022] Open
Abstract
Developing high-energy and efficient battery technologies is a crucial aspect of advancing the electrification of transportation and aviation. However, battery innovations can take years to deliver. In the case of non-aqueous battery electrolyte solutions, the many design variables in selecting multiple solvents, salts and their relative ratios make electrolyte optimization time-consuming and laborious. To overcome these issues, we propose in this work an experimental design that couples robotics (a custom-built automated experiment named "Clio") to machine-learning (a Bayesian optimization-based experiment planner named "Dragonfly"). An autonomous optimization of the electrolyte conductivity over a single-salt and ternary solvent design space identifies six fast-charging non-aqueous electrolyte solutions in two work-days and forty-two experiments. This result represents a six-fold time acceleration compared to a random search performed by the same automated experiment. To validate the practical use of these electrolytes, we tested them in a 220 mAh graphite∣∣LiNi0.5Mn0.3Co0.2O2 pouch cell configuration. All the pouch cells containing the robot-developed electrolytes demonstrate improved fast-charging capability against a baseline experiment that uses a non-aqueous electrolyte solution selected a priori from the design space.
Collapse
|
27
|
Seifrid M, Pollice R, Aguilar-Granda A, Morgan Chan Z, Hotta K, Ser CT, Vestfrid J, Wu TC, Aspuru-Guzik A. Autonomous Chemical Experiments: Challenges and Perspectives on Establishing a Self-Driving Lab. Acc Chem Res 2022; 55:2454-2466. [PMID: 35948428 PMCID: PMC9454899 DOI: 10.1021/acs.accounts.2c00220] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 01/19/2023]
Abstract
We must accelerate the pace at which we make technological advancements to address climate change and disease risks worldwide. This swifter pace of discovery requires faster research and development cycles enabled by better integration between hypothesis generation, design, experimentation, and data analysis. Typical research cycles take months to years. However, data-driven automated laboratories, or self-driving laboratories, can significantly accelerate molecular and materials discovery. Recently, substantial advancements have been made in the areas of machine learning and optimization algorithms that have allowed researchers to extract valuable knowledge from multidimensional data sets. Machine learning models can be trained on large data sets from the literature or databases, but their performance can often be hampered by a lack of negative results or metadata. In contrast, data generated by self-driving laboratories can be information-rich, containing precise details of the experimental conditions and metadata. Consequently, much larger amounts of high-quality data are gathered in self-driving laboratories. When placed in open repositories, this data can be used by the research community to reproduce experiments, for more in-depth analysis, or as the basis for further investigation. Accordingly, high-quality open data sets will increase the accessibility and reproducibility of science, which is sorely needed.In this Account, we describe our efforts to build a self-driving lab for the development of a new class of materials: organic semiconductor lasers (OSLs). Since they have only recently been demonstrated, little is known about the molecular and material design rules for thin-film, electrically-pumped OSL devices as compared to other technologies such as organic light-emitting diodes or organic photovoltaics. To realize high-performing OSL materials, we are developing a flexible system for automated synthesis via iterative Suzuki-Miyaura cross-coupling reactions. This automated synthesis platform is directly coupled to the analysis and purification capabilities. Subsequently, the molecules of interest can be transferred to an optical characterization setup. We are currently limited to optical measurements of the OSL molecules in solution. However, material properties are ultimately most important in the solid state (e.g., as a thin-film device). To that end and for a different scientific goal, we are developing a self-driving lab for inorganic thin-film materials focused on the oxygen evolution reaction.While the future of self-driving laboratories is very promising, numerous challenges still need to be overcome. These challenges can be split into cognition and motor function. Generally, the cognitive challenges are related to optimization with constraints or unexpected outcomes for which general algorithmic solutions have yet to be developed. A more practical challenge that could be resolved in the near future is that of software control and integration because few instrument manufacturers design their products with self-driving laboratories in mind. Challenges in motor function are largely related to handling heterogeneous systems, such as dispensing solids or performing extractions. As a result, it is critical to understand that adapting experimental procedures that were designed for human experimenters is not as simple as transferring those same actions to an automated system, and there may be more efficient ways to achieve the same goal in an automated fashion. Accordingly, for self-driving laboratories, we need to carefully rethink the translation of manual experimental protocols.
Collapse
Affiliation(s)
- Martin Seifrid
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Robert Pollice
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Zamyla Morgan Chan
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Acceleration
Consortium, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kazuhiro Hotta
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Science
& Innovation Center, Mitsubishi Chemical
Corporation, 1000 Kamoshidacho, Aoba, Yokohama, Kanagawa 227-8502, Japan
| | - Cher Tian Ser
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jenya Vestfrid
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Tony C. Wu
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department
of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department
of Materials Science, University of Toronto, Toronto, Ontario M5S 3E4, Canada
- Vector
Institute for Artificial Intelligence, Toronto, Ontario M5S 1M1, Canada
- Lebovic
Fellow, Canadian Institute for Advanced
Research, Toronto, Ontario M5S 1M1, Canada
| |
Collapse
|
28
|
Thangamuthu M, Ruan Q, Ohemeng PO, Luo B, Jing D, Godin R, Tang J. Polymer Photoelectrodes for Solar Fuel Production: Progress and Challenges. Chem Rev 2022; 122:11778-11829. [PMID: 35699661 PMCID: PMC9284560 DOI: 10.1021/acs.chemrev.1c00971] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Converting solar energy to fuels has attracted substantial interest over the past decades because it has the potential to sustainably meet the increasing global energy demand. However, achieving this potential requires significant technological advances. Polymer photoelectrodes are composed of earth-abundant elements, e.g. carbon, nitrogen, oxygen, hydrogen, which promise to be more economically sustainable than their inorganic counterparts. Furthermore, the electronic structure of polymer photoelectrodes can be more easily tuned to fit the solar spectrum than inorganic counterparts, promising a feasible practical application. As a fast-moving area, in particular, over the past ten years, we have witnessed an explosion of reports on polymer materials, including photoelectrodes, cocatalysts, device architectures, and fundamental understanding experimentally and theoretically, all of which have been detailed in this review. Furthermore, the prospects of this field are discussed to highlight the future development of polymer photoelectrodes.
Collapse
Affiliation(s)
- Madasamy Thangamuthu
- Department
of Chemical Engineering, University College
London, Torrington Place, London WC1E 7JE, U.K.
| | - Qiushi Ruan
- School
of Materials Science and Engineering, Southeast
University, Nanjing 211189, China
| | - Peter Osei Ohemeng
- Department
of Chemistry, The University of British
Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Bing Luo
- School
of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- International
Research Center for Renewable Energy & State Key Laboratory of
Multiphase Flow in Power Engineering, Xi’an
Jiaotong University, Xi’an 710049, China
| | - Dengwei Jing
- International
Research Center for Renewable Energy & State Key Laboratory of
Multiphase Flow in Power Engineering, Xi’an
Jiaotong University, Xi’an 710049, China
| | - Robert Godin
- Department
of Chemistry, The University of British
Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Junwang Tang
- Department
of Chemical Engineering, University College
London, Torrington Place, London WC1E 7JE, U.K.
| |
Collapse
|
29
|
Nambiar AK, Breen CP, Hart T, Kulesza T, Jamison TF, Jensen KF. Bayesian Optimization of Computer-Proposed Multistep Synthetic Routes on an Automated Robotic Flow Platform. ACS CENTRAL SCIENCE 2022; 8:825-836. [PMID: 35756374 PMCID: PMC9228554 DOI: 10.1021/acscentsci.2c00207] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 06/15/2023]
Abstract
Computer-aided synthesis planning (CASP) tools can propose retrosynthetic pathways and forward reaction conditions for the synthesis of organic compounds, but the limited availability of context-specific data currently necessitates experimental development to fully specify process details. We plan and optimize a CASP-proposed and human-refined multistep synthesis route toward an exemplary small molecule, sonidegib, on a modular, robotic flow synthesis platform with integrated process analytical technology (PAT) for data-rich experimentation. Human insights address catalyst deactivation and improve yield by strategic choices of order of addition. Multi-objective Bayesian optimization identifies optimal values for categorical and continuous process variables in the multistep route involving 3 reactions (including heterogeneous hydrogenation) and 1 separation. The platform's modularity, robotic reconfigurability, and flexibility for convergent synthesis are shown to be essential for allowing variation of downstream residence time in multistep flow processes and controlling the order of addition to minimize undesired reactivity. Overall, the work demonstrates how automation, machine learning, and robotics enhance manual experimentation through assistance with idea generation, experimental design, execution, and optimization.
Collapse
Affiliation(s)
- Anirudh
M. K. Nambiar
- Department
of Chemical Engineering, Massachusetts Institute
of Technology,77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christopher P. Breen
- Department
of Chemistry, Massachusetts Institute of
Technology,77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Travis Hart
- Department
of Chemical Engineering, Massachusetts Institute
of Technology,77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Timothy Kulesza
- Department
of Chemical Engineering, Massachusetts Institute
of Technology,77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Timothy F. Jamison
- Department
of Chemistry, Massachusetts Institute of
Technology,77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Klavs F. Jensen
- Department
of Chemical Engineering, Massachusetts Institute
of Technology,77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
30
|
Kumar R. Materiomically Designed Polymeric Vehicles for Nucleic Acids: Quo Vadis? ACS APPLIED BIO MATERIALS 2022; 5:2507-2535. [PMID: 35642794 DOI: 10.1021/acsabm.2c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite rapid advances in molecular biology, particularly in site-specific genome editing technologies, such as CRISPR/Cas9 and base editing, financial and logistical challenges hinder a broad population from accessing and benefiting from gene therapy. To improve the affordability and scalability of gene therapy, we need to deploy chemically defined, economical, and scalable materials, such as synthetic polymers. For polymers to deliver nucleic acids efficaciously to targeted cells, they must optimally combine design attributes, such as architecture, length, composition, spatial distribution of monomers, basicity, hydrophilic-hydrophobic phase balance, or protonation degree. Designing polymeric vectors for specific nucleic acid payloads is a multivariate optimization problem wherein even minuscule deviations from the optimum are poorly tolerated. To explore the multivariate polymer design space rapidly, efficiently, and fruitfully, we must integrate parallelized polymer synthesis, high-throughput biological screening, and statistical modeling. Although materiomics approaches promise to streamline polymeric vector development, several methodological ambiguities must be resolved. For instance, establishing a flexible polymer ontology that accommodates recent synthetic advances, enforcing uniform polymer characterization and data reporting standards, and implementing multiplexed in vitro and in vivo screening studies require considerable planning, coordination, and effort. This contribution will acquaint readers with the challenges associated with materiomics approaches to polymeric gene delivery and offers guidelines for overcoming these challenges. Here, we summarize recent developments in combinatorial polymer synthesis, high-throughput screening of polymeric vectors, omics-based approaches to polymer design, barcoding schemes for pooled in vitro and in vivo screening, and identify materiomics-inspired research directions that will realize the long-unfulfilled clinical potential of polymeric carriers in gene therapy.
Collapse
Affiliation(s)
- Ramya Kumar
- Department of Chemical & Biological Engineering, Colorado School of Mines, 1613 Illinois St, Golden, Colorado 80401, United States
| |
Collapse
|