arXiv subjects

Bingqing Cheng

Publications and source records attributed to Bingqing Cheng.

At least 37 records · Page 2Linked to original sources

arXiv2024

Learning charges and long-range interactions from energies and forces

Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of materials and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. Extending LES, we incorporate the ability to learn physical partial charges, encode charge states, and the option to impose charge neutrality constraints. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquid, electrolyte solution, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Our results show that LES can effectively infer physical partial charges, dipole and quadrupole moments, as well as achieve better accuracy compared to methods that explicitly learn charges. LES thus provides an efficient, interpretable, and generalizable MLIP framework for simulating complex systems with intricate charge transfer and long-range

physics.comp-ph↗

arXiv2024

Cartesian atomic cluster expansion for machine learning interatomic potentials

Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modelling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, and then use Clebsch-Gordan contraction to maintain rotational symmetry, which may introduce redundancies in representations and computational overhead. We propose an alternative: a Cartesian-coordinates-based atomic density expansion. This approach provides a complete set of polynormially indepedent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys.

physics.comp-ph↗

arXiv2024

Response Matching for generating materials and molecules

Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation, rotation, and periodicity. Here, we present a novel generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Consequently, any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching to such response is closely related to score matching in diffusion models. By employing the combination of a machine learning interatomic potential and random structure search as the denoising model, RM exploits the locality of atomic interactions, and inherently respects permutation, translation, rotation, and periodic invariances. RM is the first model to handle both molecules and bulk materials under the same framework. We demonstrate the efficiency and generalization of RM across three systems: a small organic molecular dataset, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration.

cs.LG↗

arXiv2024

Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures

An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult, due to the complexities and convergence problems in Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method, and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes or the lack of in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes, and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.

physics.chem-ph↗

arXiv2023

A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals

Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.

cond-mat.stat-mech↗

arXiv2023

Water dissociation on pristine low-index TiO2 surfaces

Water absorption and dissociation processes on pristine low-index TiO$_2$ interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO$_2$ surfaces, based on three density-functional-theory approximations. We compute the water dissociation free energies on seven pristine TiO$_2$ surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) surfaces favor water dissociation, anatase (101) and rutile (100) surfaces have mostly molecular absorption, while the calculated dissociation fraction on rutile (110) surface may depend on the density functional assumed. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. Our finding thus demonstrates that the different pristine TiO$_2$ surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.

cond-mat.mtrl-sci↗

arXiv2023

GAUCHE: A Library for Gaussian Processes in Chemistry

We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to chemical representations, however, is nontrivial, necessitating kernels defined over structured inputs such as graphs, strings and bit vectors. By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry. Motivated by scenarios frequently encountered in experimental chemistry, we showcase applications for GAUCHE in molecular discovery and chemical reaction optimisation. The codebase is made available at https://github.com/leojklarner/gauche

physics.chem-ph↗

arXiv2023

Computing chemical potentials of adsorbed or confined fluids

The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration and free energy perturbation, for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework (MOF) and water in carbon nanotubes.

cond-mat.stat-mech↗

arXiv2022

Diamond formation from hydrocarbon mixtures in planets

Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the diamond nucleation rate in pure liquid carbon, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where diamond can form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, we find a depletion zone at pressures above 200~GPa and temperatures below 3000~K-3500~K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.

cond-mat.mtrl-sci↗

arXiv2022

Onset of metallic transition in molecular liquid hydrogen

Liquid-liquid phase transition of hydrogen is at the center of hydrogen phase diagram as a promising route towards emergent properties such as the Wigner-Huntington metallization, superconductivity, and superfluidity. Here we report a study on the liquid-liquid phase transition of hydrogen using the state-of-the-art diffusion quantum Monte Carlo and density functional theory calculations. Our results suggest that the metallization process happens at lower pressures and temperatures compared to the structural phase transition of molecular to atomic hydrogen. The consequence is that metallized molecular hydrogen is stable at a wide range of pressures and temperatures. Our study breaks the conventional assumption that metallization coinciding with dissociation of hydrogen molecule, and the molecular metallic hydrogen liquid phase is likely to become the frontier of studying hydrogen phase transitions.

cond-mat.mtrl-sci↗

arXiv2022

Ranking the information content of distance measures

Real-world data typically contain a large number of features that are often heterogeneous in nature, relevance, and also units of measure. When assessing the similarity between data points, one can build various distance measures using subsets of these features. Using the fewest features but still retaining sufficient information about the system is crucial in many statistical learning approaches, particularly when data are sparse. We introduce a statistical test that can assess the relative information retained when using two different distance measures, and determine if they are equivalent, independent, or if one is more informative than the other. This in turn allows finding the most informative distance measure out of a pool of candidates. The approach is applied to find the most relevant policy variables for controlling the Covid-19 epidemic and to find compact yet informative representations of atomic structures, but its potential applications are wide ranging in many branches of science.

stat.ML↗

arXiv2022

Computing chemical potentials of solutions from structure factors

The chemical potential of a component in a solution is defined as the free energy change as the amount of the component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult, because of the convergence issues in free energy methods and finite size effects. This paper presents the S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal-isobaric ensemble. The S0 method is demonstrated on the systems of binary Lennard-Jones particles, urea--water mixtures, a NaCl aqueous solution, and a high-pressure carbon-hydrogen mixture.

cond-mat.stat-mech↗

arXiv2022

Same and interconvertible high-pressure ice phases

Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our atomistic simulations show that, amongst these bcc ice phases, ices VII, VII' and X are the same thermodynamic phase under different conditions, whereas superionic ice VII'' has a first-order phase boundary with ice VII'. Moreover, at about 300 GPa, ice X transforms into the Pbcm phase with a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure insulating ices and reveals peculiar solid-solid transition mechanisms not known in other systems.

cond-mat.mtrl-sci↗

arXiv2021

BenchML: an extensible pipelining framework for benchmarking representations of materials and molecules at scale

We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, next to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.

cs.LG↗

arXiv2021

High-pressure phase behaviors of titanium dioxide revealed by a $Δ$-learning potential

Titanium dioxide has been extensively studied in the rutile or anatase phases, while its high-pressure phases are less well understood, despite that many are thought to have interesting optical, mechanical and electrochemical properties. First-principles methods such as density functional theory (DFT) are often used to compute the enthalpies of TiO$_2$ phases at 0~K, but they are expensive and thus impractical for long time-scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stablities of the various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO$_2$, we design an empirical model as a baseline, and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called $Δ$-learning potential contains long-range electrostatic interactions, and predicts the 0~K enthalpies of stable TiO$_2$ phases that are in good agreement with DFT. We construct a pressure-temperature phase diagram of TiO$_2$ in the range $0<P<70$~GPa and $100<T<1500$~K. We then simulate dynamic phase transition processes, by compressing anatase at different temperatures. At 300~K, we observe predominantly anatase-to-baddeleyite transformation at about 20~GPa, via a martensitic two-step mechanism with highly ordered and collective atomic motion. At 2000~K, anatase can transform into cotunnite around 45-55~GPa in a thermally-activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO$_2$ phases, and our method is generally applicable to other functional materials with multiple polymorphs.

cond-mat.mtrl-sci↗

arXiv2021

Predicting the phase behaviors of superionic water at planetary conditions

Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants.

physics.comp-ph↗

arXiv2021

Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems

Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.

physics.chem-ph↗

arXiv2020

Quantum-mechanical exploration of the phase diagram of water

The phase diagram of water harbours many mysteries: some of the phase boundaries are fuzzy, and the set of known stable phases may not be complete. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures $\lesssim$8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations.

cond-mat.stat-mech↗