An official website of the United States government
Nonadiabatic molecular dynamics (NA-MD) is a powerful tool to model far-from-equilibrium processes, such as photochemical reactions and charge transport. NA-MD application to condensed phase has drawn tremendous attention recently for development of next-generation energy and optoelectronic materials. Studies of condensed matter allow one to employ efficient computational tools, such as density functional theory (DFT) and classical path approximation (CPA). Still, system size and simulation timescale are strongly limited by costly ab initio calculations of electronic energies, forces, and NA couplings. We resolve the limitations by developing a fully machine learning (ML) approach in which all the above properties are obtained using neural networks based on local descriptors. The ML models correlate the target properties for NA-MD, implemented with DFT and CPA, directly to the system structure. Trained on small systems, the neural networks are applied to large systems and long timescales, extending NA-MD capabilities by orders of magnitude. We demonstrate the approach with dependence of charge trapping and recombination on defect concentration in MoS2. Defects provide the main mechanism of charge losses, resulting in performance degradation. Charge trapping slows with decreasing defect concentration; however, recombination exhibits complex dependence, conditional on whether it occurs between free or trapped charges, and relative concentrations of carriers and defects. Delocalized shallow traps can become localized with increasing temperature, changing trapping and recombination behavior. Completely based on ML, the approach bridges the gap between theoretical models and realistic experimental conditions and enables NA-MD on thousand-atom systems and many nanoseconds.
more »
« less
Differentiable rotamer sampling with molecular force fields
Abstract Molecular dynamics (MD) is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to MD, by replacing the integration of molecular systems over time with the training of generative neural networks. This neural network approach to MD enables convergence to thermodynamic equilibrium faster than traditional MD; however, critical gaps in the theory and computational feasibility of Boltzmann generators significantly reduce their usability. Here, we develop a mathematical foundation to overcome these barriers; we demonstrate that the Boltzmann generator approach is sufficiently rapid to replace traditional MD for complex macromolecules, such as proteins in specific applications, and we provide a comprehensive toolkit for the exploration of molecular energy landscapes with neural networks.
more »
« less
- Award ID(s):
- 2210963
- PAR ID:
- 10479639
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Briefings in Bioinformatics
- Volume:
- 25
- Issue:
- 1
- ISSN:
- 1467-5463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract We present a machine learning framework to train and validate neural networks to predict the anisotropic elastic response of a monoclinic organic molecular crystal known as ‐HMX in the geometrical nonlinear regime. A filtered molecular dynamic (MD) simulations database is used to train neural networks with a Sobolev norm that uses the stress measure and a reference configuration to deduce the elastic stored free energy functional. To improve the accuracy of the elasticity tangent predictions originating from the learned stored free energy, a transfer learning technique is used to introduce additional tangential constraints from the data while necessary conditions (e.g., strong ellipticity, crystallographic symmetry) for the correctness of the model are either introduced as additional physical constraints or incorporated in the validation tests. Assessment of the neural networks is based on (1) the accuracy with which they reproduce the bottom‐line constitutive responses predicted by MD, (2) the robustness of the models measured by detailed examination of their stability and uniqueness, and (3) the admissibility of the predicted responses with respect to mechanics principles in the finite‐deformation regime. We compare the training efficiency of the neural networks under different Sobolev constraints and assess the accuracy and robustness of the models against MD benchmarks for ‐HMX.more » « less
-
Non-adiabatic (NA) molecular dynamics (MD) is a powerful approach for studying far-from-equilibrium quantum dynamics in photophysical and photochemical systems. Most NA-MD methods are developed and tested with few-state models, and their validity with complex systems involving many states is not well studied. By modeling intraband equilibration and interband recombination of charge carriers in MoS2, we investigate the convergence of three popular NA-MD algorithms, fewest switches surface hopping (FSSH), global flux surface hopping (GFSH), and decoherence induced surface hopping (DISH) with the number of states. Only the standard DISH algorithm converges with the number of states and produces Boltzmann equilibrium. Unitary propagation of the wave function in FSSH and GFSH violates the Boltzmann distribution, leads to internal inconsistency between time-dependent Schrödinger equation state populations and trajectory counts, and produces non-convergent results. Introducing decoherence in FSSH and GFSH by collapsing the wave function fixes these problems. The simplified version of DISH that omits projecting out the occupied state and is applicable to few-state systems also causes problems when the number of states is increased. We discuss the algorithmic application of wave function collapse and Boltzmann detailed balance and provide detailed FSSH, GFSH, and DISH flow charts. The use of convergent NA-MD methods is highly important for modeling complicated quantum processes involving multiple states. Our findings provide the basis for investigating quantum dynamics in realistic complex systems.more » « less
-
Surface tension is a critical property that influences polymer behavior at interfaces and affects applications ranging from coatings to biomedical devices. Traditional experimental methods for measuring polymer surface tension are time-consuming, costly, and sensitive to environmental conditions. Computational approaches such as molecular dynamics (MD) simulations are valuable but computationally intensive, especially for polymers with long chains. This study investigates the use of machine learning (ML) techniques to predict polymer surface tension using different levels of molecular representation, focusing on multilinear regression (MLR), random forest (RF), and graph neural networks (GNNs). A data set of 317 homopolymers collected from the PolyInfo database is used to train and evaluate these models. Descriptors are derived at various levels of complexity, ranging from manually calculated features to graph-based representations. The GNN approach captures the intrinsic connectivity of polymer structures, while the MLR and RF models rely on manually crafted descriptors. The performance of these models is compared with experimental data, with the GNN model demonstrating superior accuracy due to its ability to directly learn from molecular graphs. Our results show that GNNs can better capture complex nonlinear relationships in polymer structures than traditional descriptorbased methods, suggesting their significant potential for accelerating polymer design and development. The study also includes validation of model predictions against molecular dynamics simulations, highlighting the potential of GNNs to accurately model polymer interfacial properties.more » « less
-
Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transitionAbstract DNA exhibits local conformational preferences that affect its ability to adopt biologically relevant conformations, such as those required for binding proteins. Traditional methods, like Markov state models and molecular dynamics (MD) simulations, have advanced our understanding but often struggle to capture these rare conformational states due to high computational demands. Here, we introduce a novel AI framework based on dynamical graphical models (DGMs), a generative machine learning approach trained on equilibrium MD data, to predict DNA conformational transitions that are never seen in the MD ensembles. By leveraging local DNA interactions, DGMs generate a comprehensive transition matrix that captures both thermodynamic and kinetic properties of unsampled states, enabling accurate predictions of rare global conformations without the need for extensive sampling. Applying this model to the B→A transition, we demonstrate that DGMs can efficiently predict sequence-dependent A-DNA preferences, achieving results that align closely with replica exchange umbrella sampling simulations. DGMs provide new insights into DNA sequence–structure relationships, paving the way for applications in DNA sequence design and optimization.more » « less
