Benjamin Xu Shi

Benjamin Xu Shi

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Benjamin Xu Shi

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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13 November 2025 in The Journal of Chemical Physics
Verified
Journal Article
Closed access
IBIlyes Batatia
Ilyes Batatia
PBPhilipp Benner
Philipp Benner
YCYuan Chiang
Yuan Chiang
AEAlin M. Elena
Alin M. Elena
DKDávid P. Kovács
Dávid P. Kovács
GCGábor Csányi
Gábor Csányi
Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science. Over the last decade or so, machine-learned force fields have transformed atomistic modeling by enabling simulations of ab initio quality over unprecedented time and length scales. However, early machine-learning (ML) force fields have largely been limited by (i) the substantial computational and human effort required to develop and validate potentials for each particular system of interest and (ii) a general lack of transferability from one chemical system to the next. Here, we show that it is possible to create a general-purpose atomistic ML model, trained on a public dataset of moderate size, that is capable of running stable molecular dynamics for a wide range of molecules and materials. We demonstrate the power of the MACE-MP-0 model—and its qualitative and at times quantitative accuracy—on a diverse set of problems in the physical sciences, including properties of solids, liquids, gases, chemical reactions, interfaces, and even the dynamics of a small protein. The model can be applied out of the box as a starting or “foundation” model for any atomistic system of interest and, when desired, can be fine-tuned on just a handful of application-specific data points to reach ab initio accuracy. Establishing that a stable force-field model can cover almost all materials changes atomistic modeling in a fundamental way: experienced users obtain reliable results much faster, and beginners face a lower barrier to entry. Foundation models thus represent a step toward democratizing the revolution in atomic-scale modeling that has been brought about by ML force fields.

9 August 2024 in Faraday Discussions
Verified
Journal Article
Open access
PDF file
HKHarveen Kaur
Harveen Kaur
FPFlaviano Della Pia
Flaviano Della Pia
IBIlyes Batatia
Ilyes Batatia
XAXavier R. Advincula
Xavier R. Advincula
BSBenjamin X. Shi
Benjamin X. Shi
VKVenkat Kapil
Venkat Kapil
Calculating sublimation enthalpies of molecular crystal polymorphs is relevant to a wide range of technological applications. However, predicting these quantities at first-principles accuracy – even with the aid of machine learning potentials – is a challenge that requires sub-kJ mol−1 accuracy in the potential energy surface and finite-temperature sampling. We present an accurate and data-efficient protocol for training machine learning interatomic potentials by fine-tuning the foundational MACE-MP-0 model and showcase its capabilities on sublimation enthalpies and physical properties of ice polymorphs. Our approach requires only a few tens of training structures to achieve sub-kJ mol−1 accuracy in the sublimation enthalpies and sub-1% error in densities at finite temperature and pressure. Exploiting this data efficiency, we perform preliminary NPT simulations of hexagonal ice at the random phase approximation level and demonstrate a good agreement with experiments. Our results show promise for finite-temperature modelling of molecular crystals with the accuracy of correlated electronic structure theory methods.

10 November 2023 in Journal of the American Chemical Society
Verified
Journal Article
Open access
BSBenjamin X. Shi
Benjamin X. Shi
AZAndrea Zen
Andrea Zen
VKVenkat Kapil
Venkat Kapil
PNPéter R. Nagy
Péter R. Nagy
AGAndreas Grüneis
Andreas Grüneis
AMAngelos Michaelides
Angelos Michaelides
The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage, and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of chemical reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy. In particular, the large cost of accurate many-body methods makes reaching converged theoretical estimates difficult, generating a wide range of values. In this work, we address this challenge, leveraging the latest advances in diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] to obtain accurate predictions for CO on MgO. These reliable theoretical estimates allow us to evaluate the inconsistencies in published temperature-programed desorption experiments, revealing that they arise from variations in employed pre-exponential factors. Utilizing this insight, we derive new experimental estimates of the (electronic) adsorption energy with a (more) precise pre-exponential factor. As a culmination of all of this effort, we are able to reach a consensus between multiple theoretical calculations and multiple experiments for the first time. In addition, we show that our recently developed cluster-based CCSD(T) approach provides a low-cost route toward achieving accurate adsorption energies. This sets the stage for affordable and reliable theoretical predictions of chemical reactions on surfaces to guide the realization of new catalysts and gas storage materials.

31 May 2024 in The Journal of Physical Chemistry Letters
Verified
Journal Article
Open access
NONiamh O’neill
Niamh O’neill
BSBenjamin X. Shi
Benjamin X. Shi
KFKara Fong
Kara Fong
AMAngelos Michaelides
Angelos Michaelides
CSChristoph Schran
Christoph Schran
The extent of ion pairing in solution is an important phenomenon to rationalize transport and thermodynamic properties of electrolytes. A fundamental measure of this pairing is the potential of mean force (PMF) between solvated ions. The relative stabilities of the paired and solvent shared states in the PMF and the barrier between them are highly sensitive to the underlying potential energy surface. However, direct application of accurate electronic structure methods is challenging, since long simulations are required. We develop wave function based machine learning potentials with the random phase approximation (RPA) and second order Møller–Plesset (MP2) perturbation theory for the prototypical system of Na and Cl ions in water. We show both methods in agreement, predicting the paired and solvent shared states to have similar energies (within 0.2 kcal/mol). We also provide the same benchmarks for different DFT functionals as well as insight into the PMF based on simple analyses of the interactions in the system.

28 March 2022 in The Journal of Chemical Physics
Verified
Journal Article
Open access
PDF file
BSBenjamin X. Shi
Benjamin X. Shi
VKVenkat Kapil
Venkat Kapil
AZAndrea Zen
Andrea Zen
JCJi Chen
Ji Chen
AAAli Alavi
Ali Alavi
AMAngelos Michaelides
Angelos Michaelides
The O vacancy (Ov) formation energy, EOv, is an important property of a metal-oxide, governing its performance in applications such as fuel cells or heterogeneous catalysis. These defects are routinely studied with density functional theory (DFT). However, it is well-recognized that standard DFT formulations (e.g., the generalized gradient approximation) are insufficient for modeling the Ov, requiring higher levels of theory. The embedded cluster method offers a promising approach to compute EOv accurately, giving access to all electronic structure methods. Central to this approach is the construction of quantum(-mechanically treated) clusters placed within suitable embedding environments. Unfortunately, current approaches to constructing the quantum clusters either require large system sizes, preventing application of high-level methods, or require significant manual input, preventing investigations of multiple systems simultaneously. In this work, we present a systematic and general quantum cluster design protocol that can determine small converged quantum clusters for studying the Ov in metal-oxides with accurate methods, such as local coupled cluster with single, double, and perturbative triple excitations. We apply this protocol to study the Ov in the bulk and surface planes of rutile TiO2 and rock salt MgO, producing the first accurate and well-converged determinations of EOv with this method. These reference values are used to benchmark exchange–correlation functionals in DFT, and we find that all the studied functionals underestimate EOv, with the average error decreasing along the rungs of Jacob’s ladder. This protocol is automatable for high-throughput calculations and can be generalized to study other point defects or adsorbates.

23 May 2025 in Chemical Science
Verified
Journal Article
Open access
PDF file
FPFlaviano Della Pia
Flaviano Della Pia
BSBenjamin X. Shi
Benjamin X. Shi
VKVenkat Kapil
Venkat Kapil
AZAndrea Zen
Andrea Zen
DADario Alfè
Dario Alfè
AMAngelos Michaelides
Angelos Michaelides
As with many parts of the natural sciences, machine learning interatomic potentials (MLIPs) are revolutionizing the modelling of molecular crystals. However, challenges remain for the accurate and efficient calculation of sublimation enthalpies – a key thermodynamic quantity measuring the stability of a molecular crystal. Specifically, two key stumbling blocks are: (i) the need for thousands of ab initio quality reference structures to generate training data; and (ii) the sometimes unreliable nature of density functional theory, the main technique for generating such data. Exploiting recent developments in foundation models for chemistry and materials science alongside accurate quantum diffusion Monte Carlo benchmarks, offers a promising path forward. Herein, we demonstrate the generation of MLIPs capable of describing molecular crystals at finite temperature and pressure with sub-chemical accuracy, using as few as ∼200 data structures; an order of magnitude improvement over the current state-of-the-art. We apply this framework to compute the sublimation enthalpies of the X23 dataset, accounting for anharmonicity and nuclear quantum effects, achieving sub-chemical accuracy with respect to experiment. Importantly, we show that our framework can be generalized to crystals of pharmaceutical relevance, including paracetamol and aspirin. Nuclear quantum effects are also accurately captured as shown for the case of squaric acid. By enabling accurate modelling at ambient conditions, this work paves the way for deeper insights into pharmaceutical and biological systems.