Engineering topics

Zou, Ziyue

Publications and source records attributed to Zou, Ziyue.

8 records

DOE OSTI2024

A graph neural network-state predictive information bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected expert-based features. Here, in this work, we present a Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) framework, which combines graph neural networks and the state predictive information bottleneck to automatically learn low-dimensional representations directly from atomic coordinates. Tested on three benchmark systems, our approach predicts essential structural, thermodynamic and kinetic information for slow processes, demonstrating robustness across diverse systems. The method shows promise for complex systems, enabling effective enhanced sampling without requiring pre-defined reaction coordinates or input features.

Zou, Ziyue↗

DOE OSTI2024

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Here, we investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture back-and-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

Chemistry↗

DOE OSTI2024

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. Our approach uses simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine from their molten states. Our graph latent variables when biased in well-tempered metadynamics consistently show transitions between states and achieve accurate free energy calculations in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our graph neural net variables for improved sampling. Furthermore, the protocol shown here should be applicable for other systems and with other sampling methods.

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DOE OSTI2024

Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution?

Even though nucleation is ubiquitous in different science and engineering problems, investigating nucleation is extremely difficult due to the complicated ranges of time and length scales involved. In this work, we simulate NaCl nucleation in both molten and aqueous environments using enhanced sampling of all-atom molecular dynamics with deep-learning-based estimation of reaction coordinates. By incorporating various structural order parameters and learning the reaction coordinate as a function thereof, we achieve significantly improved sampling relative to traditional ad hoc descriptions of what drives nucleation, particularly in an aqueous medium. Our results reveal a one-step nucleation mechanism in both environments, with reaction coordinate analysis highlighting the importance of local ion density in distinguishing solid and liquid states. However, although fluctuations in the local ion density are necessary to drive nucleation, they are not sufficient. Our analysis shows that near the transition states, descriptors such as enthalpy and local structure become crucial. Furthermore, our protocol proposed here enables robust nucleation analysis and phase sampling and could offer insights into nucleation mechanisms for generic small molecules in different environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water

Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture, elucidating the roles of different interactions in nucleation processes. In this study, we make use of three complementary techniques to disentangle the role played by short- and long-range interactions in solvent-mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Second, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Third, the deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from the LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state under ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from the combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence

With the advent of faster computer processors and especially graphics processing units (GPUs) over the last few decades, the use of data-intensive machine learning (ML) and artificial intelligence (AI) has increased greatly, and the study of crystal nucleation has been one of the beneficiaries. In this study, we outline how ML and AI have been applied to address four outstanding difficulties of crystal nucleation: how to discover better reaction coordinates (RCs) for describing accurately non-classical nucleation situations; the development of more accurate force fields for describing the nucleation of multiple polymorphs or phases for a single system; more robust identification methods for determining crystal phases and structures; and as a method to yield improved course-grained models for studying nucleation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Driving and characterizing nucleation of urea and glycine polymorphs in water

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics

Understanding the driving forces behind the nucleation of different polymorphs is of great importance for material sciences and the pharmaceutical industry. This includes understanding the reaction coordinate that governs the nucleation process and correctly calculating the relative free energies of different polymorphs. Here, we demonstrate, for the prototypical case of urea nucleation from the melt, how one can learn such a one-dimensional reaction coordinate as a function of prespecified order parameters and use it to perform efficient biased all-atom molecular dynamics simulations. The reaction coordinate is learnt as a function of the generic thermodynamic and structural order parameters using the “spectral gap optimization of order parameters (SGOOP)” approach [Tiwary, P. and Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. (2016)] and is biased using well-tempered metadynamics simulations. The reaction coordinate gives insights into the role played by different structural and thermodynamics order parameters, and the biased simulations obtain accurate relative free energies for different polymorphs. This includes an accurate prediction of the approximate pressure at which urea undergoes a phase transition and one of the metastable polymorphs becomes the most stable conformation. Here, we believe the ideas demonstrated in this work will facilitate efficient sampling of nucleation in complex, generic systems.

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