Publications

Submitted
Yu Xie, Jonathan Vandermause, Lixin Sun, Andrea Cepellotti, and Boris Kozinsky. Submitted. “Fast Bayesian Force Fields from Active Learning: Study of Inter-Dimensional Transformation of Stanene”. Publisher's VersionAbstract
We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, capable of simulating millions of atoms. Using this approach, we perform large scale molecular dynamics simulations of the stability of the stanene monolayer. We discover an unusual phase transformation mechanism of 2D stanene, where ripples lead to nucleation of bilayer defects, densification into a disordered multilayer structure, followed by formation of bulk liquid at high temperature or nucleation and growth of the 3D bcc crystal at low temperature. The presented method opens possibilities for rapid development of fast accurate uncertainty-aware models for simulating long-time large-scale dynamics of complex materials.
Simon Batzner, Tess E. Smidt, Lixin Sun, Jonathan Mailoa, Mordechai Kornbluth, Nicola Molinari, and Boris Kozinsky. Submitted. “SE(3)-Equivariant Graph Neural Networks for Data-Efficienct and Accurate Interatomic Potentials”. PreprintAbstract
This work presents Neural Equivariant Interatomic Potentials (NequIP), a SE(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs SE(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging set of diverse molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.
nequip.pdf
Nicola Molinari, Yu Xie, Ian Leifer, Mordechai Kornbluth, and Boris Kozinsky. Submitted. “Spectral de-noising for calculating correlated transport properties”. Publisher's VersionAbstract
Computation of correlated ionic transport properties from molecular dynamics in the Green-Kubo formalism is expensive as one cannot rely on the affordable mean square displacement approach. We use spectral decomposition of the short-time ionic displacement covariance to learn a set of diffusion eigenmodes that encode the correlation structure and form a basis for analyzing the ionic trajectories. This allows to systematically reduce the uncertainty and accelerate computations of ionic conductivity in systems with a steady-state correlation structure. We provide mathematical and numerical proofs of the method's robustness, and demonstrate it on realistic electrolyte materials.
2020
Jin Soo Lim, Jonathan Vandermause, Matthijs A. Van Spronsen, Albert Musaelian, Christopher R. O'Connor, Tobias Egle, Yu S. Xie, Lixin Sun, Nicola Molinari, Jacob Florian, Kaining Duanmu, Robert Madix, Philippe Sautet, Cynthia M. Friend, and Boris Kozinsky. 8/14/2020. “Evolution of Metastable Structures at Bimetallic Surfaces from Microscopy and Machine-Learning Molecular Dynamics.” Journal of the American Chemical Society. Publisher's VersionAbstract
Restructuring of interfaces plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. By developing and performing accelerated machine-learning molecular dynamics followed by an automated analysis method, we discover and characterize previously unidentified surface restructuring mechanisms in an unbiased fashion, including Pd-Ag place exchange and Ag pop-out, as well as step ascent and descent. Remarkably, layer-by-layer dissolution of Pd into Ag is always preceded by an encapsulation of Pd islands by Ag, resulting in a significant migration of Ag out of the surface and a formation of extensive vacancy pits within a period of microseconds. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. Our approach is broadly applicable to complex multimetallic systems and enables the previously intractable mechanistic investigation of restructuring dynamics at atomic resolution.
jacs.0c06401.pdf
Jonathan Vandermause, Steven B Torrisi, Simon Batzner, Yu Xie, Lixin Sun, Alexie M Kolpak, and Boris Kozinsky. 3/18/2020. “On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events.” NPJ Comput Mater. Publisher's VersionAbstract
Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations, which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the model. This severely limits the practical application of these models in systems with dynamics governed by important rare events, such as chemical reactions and diffusion. We present an adaptive Bayesian inference method for automating the training of interpretable, low-dimensional, and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics simulations. Within an active learning framework, the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the model. The method is applied to a range of single- and multi-element systems and shown to achieve a favorable balance of accuracy and computational efficiency, while requiring a minimal amount of ab initio training data. We provide a fully open-source implementation of our method, as well as a procedure to map trained models to computationally efficient tabulated force fields.
flare_npj.pdf
Nicola Molinari and Boris Kozinsky. 3/12/2020. “Chelation-induced reversal of negative cation transference number in ionic-liquid electrolytes.” The Journal of Physical Chemistry. Publisher's VersionAbstract
Strong anion–cation interaction in lithium-salt/ionic liquid electrolytes leads to ionic association that decreases the Li transference number, even causing it to be negative. We show that these interactions can be greatly reduced by adding cyclic ethylene oxide molecules, and we quantitatively examine the effect using rigorous multispecies concentrated solution theory coupled with molecular dynamics simulations. The added molecules, primarily lithium ionophore V also known as 12-crown-4, have high affinity to lithium, therefore disrupting the lithium cation–anion coupling, resulting in a significantly improved transference number. First, we investigate the lithium–anion spatial correlation by studying their clusters and show that the 12-crown-4 ether allows the formation of previously nonexisting positively charged lithium-containing complexes. We then prove that the chelators actively compete with the anion to coordinate lithium ions by showing that the persistence-over-time of a given anion coordination cage decreases when ionophore molecules are added to the system. Last, we report an increase in the lithium transference number for a variety of chemistries as a function of added 12-crown-4 (and another ionophore, 18-crown-6) molecules, and even positive values can be reached. Our results provide a foundation for new design and optimization strategies to reverse the sign of and increase the transference number in highly correlated concentrated electrolytes.
Chelation-Induced_Reversal_of_Negative_Cation_Transference_Number_in_Ionic_Liquid_Electrolytes.pdf
2019
Jonathan P Mailoa, Mordechai Kornbluth, Simon L Batzner, Georgy Samsonidze, Stephen T Lam, Jonathan Vandermause, Chris Ablitt, Nicola Molinari, and Boris Kozinsky. 9/30/2019. “A fast neural network approach for direct covariant forces prediction in complex multi-element extended systems.” Nature Machine Intelligence, 1, Pp. 471-479. Publisher's VersionAbstract
Neural network force field (NNFF) is a method for performing regression on atomic structure–force relationships, bypassing the expensive quantum mechanics calculations that prevent the execution of long ab initio quality molecular dynamics (MD) simulations. However, most NNFF methods for complex multi-element atomic systems indirectly predict atomic force vectors by exploiting just atomic structure rotation-invariant features and network-feature spatial derivatives, which are computationally expensive. Here, we show a staggered NNFF architecture that exploits both rotation-invariant and -covariant features to directly predict atomic force vectors without using spatial derivatives, and we demonstrate 2.2× NNFF–MD acceleration over a state-of-the-art C++ engine using a Python engine. This fast architecture enables us to develop NNFF for complex ternary- and quaternary-element extended systems composed of long polymer chains, amorphous oxide and surface chemical reactions. The rotation-invariant–covariant architecture described here can also directly predict complex covariant vector outputs from local environments, in other domains beyond computational material science.
A_fast_neural_network_approach_for_direct_covariant_forces_prediction_in_complex_multi-element_extended_systems.pdf
Mordechai Kornbluth, Jonathan Mailoa, Boris Kozinsky, Georgy Samsonidze, and John F Christensen. 2019. “Amorphous LiF as an Artificial SEI Layer for Lithium Batteries.” United States of America. us20190036120a1.pdf
Jin Soo Lim, Nicola Molinari, Kaining Duanmu, Philippe Sautet, and Boris Kozinsky. 2019. “Automated detection and characterization of surface restructuring events in bimetallic catalysts.” The Journal of Physical Chemistry C. lim_et_al._-_2019_-_automated_detection_and_characterization_of_surface_restructuring_events_in_bimetallic_catalysts.pdf
Paul Le Floch, Nicola Molinari, Kewang Nan, Shuwen Zhang, Boris Kozinsky, Zhigang Suo, and Jia Liu. 2019. “Fundamental limits to the electrochemical impedance stability of dielectric elastomers in bioelectronics.” Nano letters. lefloch.pdf
Nicola Molinari, Jonathan Pradana Mailoa, and Boris Kozinsky. 2019. “General Trend of Negative Li Effective Charge in Ionic Liquid Electrolytes.” The journal of physical chemistry letters. molinari_mailoa_kozinsky_-_2019_-_general_trend_of_a_negative_li_effective_charge_in_ionic_liquid_electrolytes.pdf
Malar Azagarsamy, Kulandaivelu Sivanandan, Hany Basam Eitouni, Jonathan P Mailoa, Georgy Samsonidze, Karim R Gadelrab, and Boris Kozinsky. 2019. “Poly (anhydride)-based polymer electrolytes for high voltage lithium ion batteries.” United States of America. us20190131653a1.pdf
Malar Azagarsamy, Kulandaivelu Sivanandan, Hany Basam Eitouni, Jonathan P Mailoa, Georgy Samsonidze, Karim R Gadelrab, and Boris Kozinsky. 2019. “Poly (ketone)-based polymer electrolytes for high voltage lithium ion batteries.” United States of America. us20190190067a1.pdf
Daehyun Wee, Jeeyoung Kim, Semi Bang, Georgy Samsonidze, and Boris Kozinsky. 2019. “Quantification of uncertainties in thermoelectric properties of materials from a first-principles prediction method: An approach based on Gaussian process regression.” Physical Review Materials, 3, 3, Pp. 033803. wee_et_al._-_2019_-_quantification_of_uncertainties_in_thermoelectric_properties_of_materials_from_a_first-principles_prediction_method.pdf
Eric R Fadel, Francesco Faglioni, Georgy Samsonidze, Nicola Molinari, Boris V Merinov, William A Goddard III, Jeffrey C Grossman, Jonathan P Mailoa, and Boris Kozinsky. 2019. “Role of solvent-anion charge transfer in oxidative degradation of battery electrolytes.” Nature communications, 10. fadel_et_al._-_2019_-_role_of_solvent-anion_charge_transfer_in_oxidative_degradation_of_battery_electrolytes.pdf
Nicola Molinari, Jonathan P Mailoa, Nathan Craig, Jake Christensen, and Boris Kozinsky. 2019. “Transport anomalies emerging from strong correlation in ionic liquid electrolytes.” Journal of Power Sources, 428, Pp. 27–36. molinari_et_al._-_2019_-_transport_anomalies_emerging_from_strong_correlation_in_ionic_liquid_electrolytes.pdf
Leonid Kahle, Albert Musaelian, Nicola Marzari, and Boris Kozinsky. 2019. “Unsupervised landmark analysis for jump detection in molecular dynamics simulations.” Physical Review Materials, 3, 5, Pp. 055404. kahle_et_al._-_2019_-_unsupervised_landmark_analysis_for_jump_detection_in_molecular_dynamics_simulations.pdf
2018
Georgy Samsonidze and Boris Kozinsky. 2018. “Accelerated Screening of Thermoelectric Materials by First-Principles Computations of Electron–Phonon Scattering.” Advanced Energy Materials, 8, 20, Pp. 1800246. samsonidze_et_al-2018-advanced_energy_materials.pdf
Daniel J Brooks, Boris V Merinov, William A Goddard III, Boris Kozinsky, and Jonathan Mailoa. 2018. “Atomistic Description of Ionic Diffusion in PEO–LiTFSI: Effect of Temperature, Molecular Weight, and Ionic Concentration.” Macromolecules, 51, 21, Pp. 8987–8995. brooks_et_al._-_2018_-_atomistic_description_of_ionic_diffusion_in_peo-litfsi_effect_of_temperature_molecular_weight_and_ionic_conce.pdf
John F Christensen, Boris Kozinsky, and Sondra Hellstrom. 2018. “Coated Cathode Active Material for Engineered Solid-State Battery Interfaces.” United States of America. us20180083315a1.pdf

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