ArticleProceedings of the National Academy of Sciences of the United States of America2023
Driving and characterizing nucleation of urea and glycine polymorphs in water.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mechanistic Insights into Molecular Modifiers That Promote Urate Crystallization through Solute Assembly Regulation.JACS Au · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics.The journal of physical chemistry. B · 2025Article
- Deciphering the complexities of crystalline state(s) with molecular simulations.Communications chemistry · 2025Review
- Guanine Crystallization by Particle Attachment.Journal of the American Chemical Society · 2025Article
- Enhanced polymorph metastability drives glycine nucleation in aqueous salt solutions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- On the role of α-alumina in the origin of life: Surface-driven assembly of amino acids.Science advances · 2025Article
- The effect of salt additives on the glycine crystallization pathway revealed by studying one crystal nucleation at a time.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.Journal of chemical theory and computation · 2024Article
- Article
- Thermodynamics-inspired explanations of artificial intelligence.Nature communications · 2024Article
- Calculating Protein-Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling.Journal of chemical theory and computation · 2024Article
- Influence of Solvent Selection on the Crystallizability and Polymorphic Selectivity Associated with the Formation of the "Disappeared" Form I Polymorph of Ritonavir.Molecular pharmaceutics · 2024Article
- Information Bottleneck Approach for Markov Model Construction.Journal of chemical theory and computation · 2024Article
- Article
- Enhanced Sampling with Machine Learning.Annual review of physical chemistry · 2024Review
- Calculating Protein-Ligand Residence Times Through State Predictive Information Bottleneck based Enhanced Sampling.bioRxiv : the preprint server for biology · 2024Article
- Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE.Journal of chemical information and modeling · 2024Article
- Machine Learning Nucleation Collective Variables with Graph Neural Networks.Journal of chemical theory and computation · 2024Article
- Article
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4 authors.
Funding
Abstract
Crystal nucleation is relevant across the domains of fundamental and applied sciences. However, in many cases, its mechanism remains unclear due to a lack of temporal or spatial resolution. To gain insights into the molecular details of nucleation, some form of molecular dynamics simulations is typically performed; these simulations, in turn, are limited by their ability to run long enough to sample the nucleation event thoroughly. To overcome the timescale limits in typical molecular dynamics simulations in a manner free of prior human bias, here, we employ the machine learning-augmented molecular dynamics framework "reweighted autoencoded variational Bayes for enhanced sampling (RAVE)." We study two molecular systems-urea and glycine-in explicit all-atom water, due to their enrichment in polymorphic structures and common utility in commercial applications. From our simulations, we observe multiple back-and-forth nucleation events of different polymorphs from homogeneous solution; from these trajectories, we calculate the relative ranking of finite-sized polymorph crystals embedded in solution, in terms of the free-energy difference between the finite-sized crystal polymorph and the original solution state. We further observe that the obtained reaction coordinates and transitions are highly nonclassical.
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