Polymer sequence design via molecular simulation-based active learning

Ramesh, Praneeth S.; Patra, Tarak K.

doi:10.1039/d2sm01193j

Polymer sequence design via molecular simulation-based active learning

Journal Article · 01 January 2023 · Soft Matter

DOI:https://doi.org/10.1039/d2sm01193j· OSTI ID:2423243

Ramesh, Praneeth S. ^[1]; ^[1]

Department of Chemical Engineering, Center for Atomistic Modeling and Materials Design and Center for Carbon Capture Utilization and Storage, Indian Institute of Technology Madras, Chennai, TN 600036, India

We present a thorough analysis of active learning strategies for polymer sequence engineering and design.

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Argonne Leadership Computing Facility (ALCF)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 2423243

Journal Information:: Soft Matter, Journal Name: Soft Matter Journal Issue: 2 Vol. 19; ISSN SMOABF; ISSN 1744-683X

Publisher:: Royal Society of Chemistry

Country of Publication:: United States

Language:: English

References (54)

Machine learning in combinatorial polymer chemistry Gormley, Adam J.; Webb, Michael A. Nature Reviews Materials, Vol. 6, Issue 8 https://doi.org/10.1038/s41578-021-00282-3	journal	February 2021
Sequence Effects on the Glass Transition of a Model Copolymer System Drayer, William F.; Simmons, David S. Macromolecules, Vol. 55, Issue 14 https://doi.org/10.1021/acs.macromol.2c00664	journal	July 2022
Opportunities and Challenges for Inverse Design of Nanostructures with Sequence Defined Macromolecules Reinhart, Wesley F.; Statt, Antonia Accounts of Materials Research, Vol. 2, Issue 9 https://doi.org/10.1021/accountsmr.1c00089	journal	August 2021
Unsupervised learning of sequence-specific aggregation behavior for a model copolymer Statt, Antonia; Kleeblatt, Devon C.; Reinhart, Wesley F. Soft Matter, Vol. 17, Issue 33 https://doi.org/10.1039/D1SM01012C	journal	January 2021
Adaptive Strategies for Materials Design using Uncertainties Balachandran, Prasanna V.; Xue, Dezhen; Theiler, James Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep19660	journal	January 2016
Sequence‐defined Pareto frontier of a copolymer structure Bale, Ashwin A.; Gautham, Sachin M. B.; Patra, Tarak K. Journal of Polymer Science, Vol. 60, Issue 14 https://doi.org/10.1002/pol.20220088	journal	April 2022
Collapse Transition in Random Copolymer Solutions Dasmahapatra, Ashok Kumar; Kumaraswamy, Guruswamy; Nanavati, Hemant Macromolecules, Vol. 39, Issue 26 https://doi.org/10.1021/ma061017q	journal	December 2006
Synthesis of Monodisperse Sequence-Coded Polymers with Chain Lengths above DP100 Al Ouahabi, Abdelaziz; Kotera, Mitsuharu; Charles, Laurence ACS Macro Letters, Vol. 4, Issue 10 https://doi.org/10.1021/acsmacrolett.5b00606	journal	September 2015
Bias free multiobjective active learning for materials design and discovery Jablonka, Kevin Maik; Jothiappan, Giriprasad Melpatti; Wang, Shefang Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22437-0	journal	April 2021
Featurization strategies for polymer sequence or composition design by machine learning Patel, Roshan A.; Borca, Carlos H.; Webb, Michael A. Molecular Systems Design & Engineering, Vol. 7, Issue 6 https://doi.org/10.1039/D1ME00160D	journal	January 2022
Microwave-Assisted Solid-Phase Synthesis of Peptoids Olivos, Hernando J.; Alluri, Prasanna G.; Reddy, M. Muralidhar Organic Letters, Vol. 4, Issue 23 https://doi.org/10.1021/ol0267578	journal	November 2002
Pathway to copolymer collapse in dilute solution: Uniform versus random distribution of comonomers Dasmahapatra, Ashok Kumar; Nanavati, Hemant; Kumaraswamy, Guruswamy The Journal of Chemical Physics, Vol. 127, Issue 23 https://doi.org/10.1063/1.2802296	journal	December 2007
Model for disordered proteins with strongly sequence-dependent liquid phase behavior Statt, Antonia; Casademunt, Helena; Brangwynne, Clifford P. The Journal of Chemical Physics, Vol. 152, Issue 7 https://doi.org/10.1063/1.5141095	journal	February 2020
Direct Comparisons of X-ray Scattering and Atomistic Molecular Dynamics Simulations for Precise Acid Copolymers and Ionomers Buitrago, C. Francisco; Bolintineanu, Dan S.; Seitz, Michelle E. Macromolecules, Vol. 48, Issue 4 https://doi.org/10.1021/ma5022117	journal	January 2015
Sequence and entropy-based control of complex coacervates Chang, Li-Wei; Lytle, Tyler K.; Radhakrishna, Mithun Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01249-1	journal	November 2017
Predicting aggregate morphology of sequence-defined macromolecules with recurrent neural networks Bhattacharya, Debjyoti; Kleeblatt, Devon C.; Statt, Antonia Soft Matter, Vol. 18, Issue 27 https://doi.org/10.1039/D2SM00452F	journal	January 2022
Targeted sequence design within the coarse-grained polymer genome Webb, Michael A.; Jackson, Nicholas E.; Gil, Phwey S. Science Advances, Vol. 6, Issue 43 https://doi.org/10.1126/sciadv.abc6216	journal	October 2020
Statistical inference and adaptive design for materials discovery Lookman, Turab; Balachandran, Prasanna V.; Xue, Dezhen Current Opinion in Solid State and Materials Science, Vol. 21, Issue 3 https://doi.org/10.1016/j.cossms.2016.10.002	journal	June 2017
Hierarchical Shape-Specified Model Polymer Nanoparticles via Copolymer Sequence Control Tulsi, Davindra K.; Simmons, David S. Macromolecules, Vol. 55, Issue 6 https://doi.org/10.1021/acs.macromol.1c02215	journal	March 2022
Designing Sequence-Specific Copolymer Compatibilizers Using a Molecular-Dynamics-Simulation-Based Genetic Algorithm Meenakshisundaram, Venkatesh; Hung, Jui-Hsiang; Patra, Tarak K. Macromolecules, Vol. 50, Issue 3 https://doi.org/10.1021/acs.macromol.6b01747	journal	January 2017
Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation Kremer, Kurt; Grest, Gary S. The Journal of Chemical Physics, Vol. 92, Issue 8 https://doi.org/10.1063/1.458541	journal	April 1990
Coil-to-globule transitions of homopolymers and multiblock copolymers Wang, Wei; Zhao, Peng; Yang, Xi The Journal of Chemical Physics, Vol. 141, Issue 24 https://doi.org/10.1063/1.4904888	journal	December 2014
Data-Driven Methods for Accelerating Polymer Design Patra, Tarak K. ACS Polymers Au, Vol. 2, Issue 1 https://doi.org/10.1021/acspolymersau.1c00035	journal	December 2021
Importance of Feature Selection in Machine Learning and Adaptive Design for Materials Balachandran, Prasanna V.; Xue, Dezhen; Theiler, James Materials Discovery and Design https://doi.org/10.1007/978-3-319-99465-9_3	book	January 2018
Sequence-defined bioactive macrocycles via an acid-catalysed cascade reaction Porel, Mintu; Thornlow, Dana N.; Phan, Ngoc N. Nature Chemistry, Vol. 8, Issue 6 https://doi.org/10.1038/nchem.2508	journal	May 2016
The viscosity-radius relationship for concentrated polymer solutions Dunstan, Dave E. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-36596-6	journal	January 2019
Synthesis of Molecularly Encoded Oligomers Using a Chemoselective “AB + CD” Iterative Approach Trinh, Thanh Tam; Oswald, Laurence; Chan-Seng, Delphine Macromolecular Rapid Communications, Vol. 35, Issue 2 https://doi.org/10.1002/marc.201300774	journal	December 2013
Discovery of Energy Storage Molecular Materials Using Quantum Chemistry-Guided Multiobjective Bayesian Optimization Agarwal, Garvit; Doan, Hieu A.; Robertson, Lily A. Chemistry of Materials, Vol. 33, Issue 20 https://doi.org/10.1021/acs.chemmater.1c02040	journal	October 2021
Phase behavior and structure formation in linear multiblock copolymer solutions by Monte Carlo simulation Gindy, Marian E.; Prud’homme, Robert K.; Panagiotopoulos, Athanassios Z. The Journal of Chemical Physics, Vol. 128, Issue 16 https://doi.org/10.1063/1.2905231	journal	April 2008
A Coarse-Grained Protein Model in a Water-like Solvent Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V. Scientific Reports, Vol. 3, Issue 1 https://doi.org/10.1038/srep01841	journal	May 2013
Accelerating copolymer inverse design using monte carlo tree search Patra, Tarak K.; Loeffler, Troy D.; Sankaranarayanan, Subramanian K. R. S. Nanoscale, Vol. 12, Issue 46 https://doi.org/10.1039/D0NR06091G	journal	January 2020
Predicting Adhesive Free Energies of Polymer–Surface Interactions with Machine Learning Shi, Jiale; Quevillon, Michael J.; Amorim Valença, Pedro H. ACS Applied Materials & Interfaces, Vol. 14, Issue 32 https://doi.org/10.1021/acsami.2c08891	journal	August 2022
Efficient Phase Diagram Sampling by Active Learning Dai, Chengyu; Glotzer, Sharon C. The Journal of Physical Chemistry B, Vol. 124, Issue 7 https://doi.org/10.1021/acs.jpcb.9b09202	journal	January 2020
Machine Learning Strategy for Accelerated Design of Polymer Dielectrics Mannodi-Kanakkithodi, Arun; Pilania, Ghanshyam; Huan, Tran Doan Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep20952	journal	February 2016
Efficient hyperparameter tuning for kernel ridge regression with Bayesian optimization Stuke, Annika; Rinke, Patrick; Todorović, Milica Machine Learning: Science and Technology, Vol. 2, Issue 3 https://doi.org/10.1088/2632-2153/abee59	journal	June 2021
100th Anniversary of Macromolecular Science Viewpoint: Opportunities in the Physics of Sequence-Defined Polymers Perry, Sarah L.; Sing, Charles E. ACS Macro Letters, Vol. 9, Issue 2 https://doi.org/10.1021/acsmacrolett.0c00002	journal	January 2020
Data-driven discovery of cardiolipin-selective small molecules by computational active learning Mohr, Bernadette; Shmilovich, Kirill; Kleinwächter, Isabel S. Chemical Science, Vol. 13, Issue 16 https://doi.org/10.1039/D2SC00116K	journal	January 2022
Sequence-Controlled Polymers Lutz, J. -F.; Ouchi, M.; Liu, D. R. Science, Vol. 341, Issue 6146 https://doi.org/10.1126/science.1238149	journal	August 2013
Sequence-dependent self-coacervation in high charge-density polyampholytes Madinya, Jason J.; Chang, Li-Wei; Perry, Sarah L. Molecular Systems Design & Engineering, Vol. 5, Issue 3 https://doi.org/10.1039/C9ME00074G	journal	January 2020
Sequence-Engineering Polyethylene–Polypropylene Copolymers with High Thermal Conductivity Using a Molecular-Dynamics-Based Genetic Algorithm Zhou, Tianhang; Wu, Zhenghao; Chilukoti, Hari Krishna Journal of Chemical Theory and Computation, Vol. 17, Issue 6 https://doi.org/10.1021/acs.jctc.1c00134	journal	May 2021
Accelerated search for materials with targeted properties by adaptive design Xue, Dezhen; Balachandran, Prasanna V.; Hogden, John Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11241	journal	April 2016
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Polymer informatics: Current status and critical next steps Chen, Lihua; Pilania, Ghanshyam; Batra, Rohit Materials Science and Engineering: R: Reports, Vol. 144 https://doi.org/10.1016/j.mser.2020.100595	journal	April 2021
Active learning in materials science with emphasis on adaptive sampling using uncertainties for targeted design Lookman, Turab; Balachandran, Prasanna V.; Xue, Dezhen npj Computational Materials, Vol. 5, Issue 1 https://doi.org/10.1038/s41524-019-0153-8	journal	February 2019
Scoping the polymer genome: A roadmap for rational polymer dielectrics design and beyond Mannodi-Kanakkithodi, Arun; Chandrasekaran, Anand; Kim, Chiho Materials Today, Vol. 21, Issue 7 https://doi.org/10.1016/j.mattod.2017.11.021	journal	September 2018
Sequence-defined multifunctional polyethers via liquid-phase synthesis with molecular sieving Dong, Ruijiao; Liu, Ruiyi; Gaffney, Piers R. J. Nature Chemistry, Vol. 11, Issue 2 https://doi.org/10.1038/s41557-018-0169-6	journal	December 2018
A Tutorial on Bayesian Optimization of Expensive Cost Functions, with Application to Active User Modeling and Hierarchical Reinforcement Learning Brochu, Eric; Cora, Vlad M.; de Freitas, Nando arXiv https://doi.org/10.48550/arXiv.1012.2599	preprint	January 2010
Protein-like copolymers: computer simulation Khokhlov, Alexei R.; Khalatur, Pavel G. Physica A: Statistical Mechanics and its Applications, Vol. 249, Issue 1-4 https://doi.org/10.1016/S0378-4371(97)00473-1	journal	January 1998
Coarse-grained molecular-dynamics simulations of the self-assembly of pentablock copolymers into micelles Chushak, Y.; Travesset, A. The Journal of Chemical Physics, Vol. 123, Issue 23 https://doi.org/10.1063/1.2137714	journal	December 2005
How priors of initial hyperparameters affect Gaussian process regression models Chen, Zexun; Wang, Bo Neurocomputing, Vol. 275 https://doi.org/10.1016/j.neucom.2017.10.028	journal	January 2018
Active learning of polarizable nanoparticle phase diagrams for the guided design of triggerable self-assembling superlattices Dasetty, Siva; Coropceanu, Igor; Portner, Joshua Molecular Systems Design & Engineering, Vol. 7, Issue 4 https://doi.org/10.1039/D1ME00187F	journal	January 2022
Designing Electrostatic Interactions via Polyelectrolyte Monomer Sequence Lytle, Tyler K.; Chang, Li-Wei; Markiewicz, Natalia ACS Central Science, Vol. 5, Issue 4 https://doi.org/10.1021/acscentsci.9b00087	journal	March 2019
Micro- to macro-phase separation transition in sequence-defined coacervates Sing, Charles E. The Journal of Chemical Physics, Vol. 152, Issue 2 https://doi.org/10.1063/1.5140756	journal	January 2020
Sequence-Defined Polymers via Orthogonal Allyl Acrylamide Building Blocks Porel, Mintu; Alabi, Christopher A. Journal of the American Chemical Society, Vol. 136, Issue 38 https://doi.org/10.1021/ja507262t	journal	September 2014

Similar Records

Related Subjects

Chemistry
Materials Science
Physics
Polymer Science

Polymer sequence design via molecular simulation-based active learning

Citation Formats

References (54)

Similar Records

Related Subjects