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1. Machine Learning for Molecular Simulation

   https://doi.org/10.1146/annurev-physchem-042018-052331  

   Noé, Frank; Tkatchenko, Alexandre; Müller, Klaus-Robert; Clementi, Cecilia (April 2020, Annual Review of Physical Chemistry)

   null (Ed.)

   Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML methods. Here we review recent ML methods for molecular simulation, with particular focus on (deep) neural networks for the prediction of quantum-mechanical energies and forces, on coarse-grained molecular dynamics, on the extraction of free energy surfaces and kinetics, and on generative network approaches to sample molecular equilibrium structures and compute thermodynamics. To explain these methods and illustrate open methodological problems, we review some important principles of molecular physics and describe how they can be incorporated into ML structures. Finally, we identify and describe a list of open challenges for the interface between ML and molecular simulation. 

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2. Towards a machine learned thermodynamics: exploration of free energy landscapes in molecular fluids, biological systems and for gas storage and separation in metal–organic frameworks

   https://doi.org/10.1039/D0ME00134A  

   Desgranges, Caroline; Delhommelle, Jerome (January 2021, Molecular Systems Design & Engineering)

   null (Ed.)

   In this review, we examine how machine learning (ML) can build on molecular simulation (MS) algorithms to advance tremendously our ability to predict the thermodynamic properties of a wide range of systems. The key thermodynamic properties that govern the evolution of a system and the outcome of a process include the entropy, the Helmholtz and the Gibbs free energy. However, their determination through advanced molecular simulation algorithms has remained challenging, since such methods are extremely computationally intensive. Combining MS with ML provides a solution that overcomes such challenges and, in turn, accelerates discovery through the rapid prediction of free energies. After presenting a brief overview of combined MS–ML protocols, we review how these approaches allow for the accurate prediction of these thermodynamic functions and, more broadly, of free energy landscapes for molecular and biological systems. We then discuss extensions of this approach to systems relevant to energy and environmental applications, i.e. gas storage and separation in nanoporous materials, such as metal–organic frameworks and covalent organic frameworks. We finally show in the last part of the review how ML models can suggest new ways to explore free energy landscapes, identify novel pathways and provide new insight into assembly processes. 

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3. Machine Learning in Small-Molecule Mass Spectrometry

   https://doi.org/10.1146/annurev-anchem-071224-082157  

   Hong, Yuhui; Ye, Yuzhen; Tang, Haixu (May 2025, Annual Review of Analytical Chemistry)

   Tandem mass spectrometry (MS/MS) is crucial for small-molecule analysis; however, traditional computational methods are limited by incomplete reference libraries and complex data processing. Machine learning (ML) is transforming small-molecule mass spectrometry in three key directions: (a) predicting MS/MS spectra and related physicochemical properties to expand reference libraries, (b) improving spectral matching through automated pattern extraction, and (c) predicting molecular structures of compounds directly from their MS/MS spectra. We review ML approaches for molecular representations [descriptors, simplified molecular-input line-entry (SMILE) strings, and graphs] and MS/MS spectra representations (using binned vectors and peak lists) along with recent advances in spectra prediction, retention time, collision cross sections, and spectral matching. Finally, we discuss ML-integrated workflows for chemical formula identification. By addressing the limitations of current methods for compound identification, these ML approaches can greatly enhance the understanding of biological processes and the development of diagnostic and therapeutic tools. 

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4. Open-source generation of sigma profiles: impact of quantum chemistry and solvation treatment on machine learning performance

   https://doi.org/10.1039/D5DD00087D  

   Salih, Fathya_Y M; Abranches, Dinis O; Maginn, Edward J; Colón, Yamil J (October 2025, Digital Discovery)

   The combination of machine learning (ML) models with chemistry-related tasks requires the description of molecular structures in a machine-readable way. The nature of these so-called molecular descriptors has a direct and major impact on the performance of ML models and remains an open problem in the field. Structural descriptors like SMILES strings or molecular graphs lack size-independence and can be memory intensive. Machine-learned descriptors can be of low dimensionality and constant size but lack physical significance and human interpretability. Sigma profiles, which are unnormalized histograms of the surface charge distributions of solvated molecules, combine physical significance with low dimensionality and size-independence, making them a suitable candidate for a universal molecular descriptor. However, their widespread adoption in ML applications requires open access to sigma profile generation, which is currently not available. This work details the development of OpenSPGen – an open-source tool for generating sigma profiles. Also presented are studies on the effect of different settings on the efficacy of the generated sigma profiles at predicting thermophysical material properties when used as inputs to a Gaussian process as a simple surrogate ML model. We find that a higher level of theory does not translate to more accurate results. We also provide further recommendations for sigma profile calculation and use in ML models. 

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5. Machine learning for parameter auto-tuning in molecular dynamics simulations: Efficient dynamics of ions near polarizable nanoparticles

   https://doi.org/10.1177/1094342019899457  

   Kadupitiya, JCS; Fox, Geoffrey C; Jadhao, Vikram (May 2020, The International Journal of High Performance Computing Applications)

   Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method based on a dynamical optimization framework bypassed this obstacle by representing the polarization charge density as virtual dynamic variables and evolving them in parallel with the physical dynamics of ions. We highlight the computational gains accessible with the integration of machine learning (ML) methods for parameter prediction in MD simulations by demonstrating how they were realized in MD simulations of ions near polarizable NPs. An artificial neural network–based regression model was integrated with MD simulation and predicted the optimal simulation timestep and optimization parameters characterizing the virtual system with 94.3% success. The ML-enabled auto-tuning of parameters generated accurate dynamics of ions for ≈ 10 million steps while improving the stability of the simulation by over an order of magnitude. The integration of ML-enhanced framework with hybrid Open Multi-Processing / Message Passing Interface (OpenMP/MPI) parallelization techniques reduced the computational time of simulating systems with thousands of ions and induced charges from thousands of hours to tens of hours, yielding a maximum speedup of ≈ 3 from ML-only acceleration and a maximum speedup of ≈ 600 from the combination of ML and parallel computing methods. Extraction of ionic structure in concentrated electrolytes near oil–water emulsions demonstrates the success of the method. The approach can be generalized to select optimal parameters in other MD applications and energy minimization problems. 

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