arXiv subjects

Julian D. Gale

Publications and source records attributed to Julian D. Gale.

10 recordsLinked to original sources

arXiv2026

From Accurate Quantum Chemistry to Converged Thermodynamics for Ion Pairing in Solution

Quantitative prediction of thermodynamic properties in solution is essential for translating atomistic simulations into reliable chemical insight. As an exemplar system, the behaviour of CaCO$_3$ in water has been widely studied to understand its mineralization in seawater, with potential implications for carbon-capture strategies. However, making accurate computational predictions has been a long-standing challenge, requiring both highly accurate electronic structure methods and extensive statistical sampling. Here, we combine advances in machine learning and electronic structure theory to fully resolve the ion pairing free energy of CaCO$_3$ with explicit solvation. We show that achieving quantitative agreement with experiment requires going beyond the standard density functional theory up to the "gold-standard" coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. We generate a set of systematically improvable models, enabling reliable insights into the initial association mechanism of Ca and CO$_3$ ions prior to nucleation while fully quantifying enthalpic and entropic effects. Our results demonstrate that CCSD(T)-level thermodynamic predictions of complex aqueous systems can now be routinely achieved.

physics.chem-ph↗

arXiv2025

Towards Routine Condensed Phase Simulations with Delta-Learned Coupled Cluster Accuracy: Application to Liquid Water

Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the electronic structure method of choice - coupled cluster theory with single, double and perturbative triple excitations [CCSD(T)] - to condensed phase systems is currently limited by its computational cost and complexity. Recent tour-de-force efforts have demonstrated that this accuracy can indeed bring simulated liquid water into close agreement with experiment using machine learning potentials (MLPs). However, achieving this remains far from routine, requiring large datasets and significant computational cost. In this work, we introduce a practical approach that combines developments in MLPs with local correlation approximations to enable routine CCSD(T)-level simulations of liquid water. When combined with nuclear quantum effects, we achieve agreement to experiments for structural and transport properties. Crucially, this approach extends beyond constant volume to constant pressure simulations, allowing fundamental properties such as the density to now be predicted by MLP-based CCSD(T) models. Importantly, the approach also handles constant pressure simulations, enabling MLP-based CCSD(T) models to predict isothermal-isobaric bulk properties, such as water's density maximum in close agreement with experiment. Encompassing tests across electronic structure, datasets and MLP architecture, this work provides a practical blueprint towards routinely developing CCSD(T)-based MLPs for the condensed phase.

physics.chem-ph↗

arXiv2025

Ab initio machine learning simulation of calcium carbonate from aqueous solutions to the solid state

A first principles machine learning model has been developed aimed at studying the formation of calcium carbonate from aqueous solution using molecular dynamics simulations. The model, dubbed SCAN-ML, reproduces accurately the potential energy surface derived from ab initio density-functional theory within the SCAN approximation for the exchange and correlation functional. A broad range of properties have been calculated relevant to ions in solution, solid phases, and the calcite/water interface. Careful comparison with results from experiments and semi-empirical force fields shows that SCAN-ML provides an excellent description of this system, surpassing state-of-the-art force fields for many properties, while providing a benchmark for many quantities that are currently beyond the reach of direct ab initio molecular dynamics. A key feature of SCAN-ML is its ability to capture chemical reactions, which reveals that calcium carbonate ion pair formation occurs predominantly via binding of calcium to bicarbonate, with the subsequent loss of a proton to water, rather than by direct association. Our model thus paves the way for the study of reactive crystallization pathways in calcium carbonate, which are currently poorly understood.

physics.chem-ph↗

arXiv2024

PLUMED Tutorials: a collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce ``PLUMED Tutorials'', a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.

physics.ed-ph↗

arXiv2019

The structure of CaSO4 nanorods -- the precursor of gypsum

Understanding the gypsum (CaSO4.2H2O) formation pathway from aqueous solution has been the subject of intensive research in the past years. This interest stems from the fact that gypsum appears to fall into a broader category of crystalline materials whose formation does not follow classical nucleation and growth theories. The pathways involve transitory precursor cluster species, yet the actual structural properties of such clusters are not very well understood. Here, we show how in situ high-energy X-ray diffraction experiments and molecular dynamics (MD) simulations can be combined to derive the structure of small CaSO4 clusters, which are precursors of crystalline gypsum. We fitted several plausible structures to the derived pair distribution functions and explored their dynamic properties using unbiased MD simulations based on both rigid ion and polarizable force fields. Determination of the structure and (meta)stability of the primary species is important from both a fundamental and applied perspective; for example, this will allow for an improved design of additives for greater control of the nucleation pathway.

cond-mat.mtrl-sci↗

arXiv2016

Free energy of ligand removal in the metal-organic framework UiO-66

We report an investigation of the "missing-linker phenomenon" in the Zr-based metal-organic framework UiO-66 using atomistic forcefield and quantum chemical methods. For a vacant benzene dicarboxylate ligand, the lowest energy charge capping mechanism involves acetic acid or Cl-/H2O. The calculated defect free energy of formation is remarkably low, consistent with the high defect concentrations reported experimentally. A dynamic structural instability is identified for certain higher defect concentrations. In addition to the changes in material properties upon defect formation, we assess the formation of molecular aggregates, which provide an additional driving force for ligand loss. These results are expected to be of relevance to a wide range of metal-organic frameworks.

cond-mat.mtrl-sci↗

arXiv2012

Calcium Carbonate Polyamorphism and Its Role in Biomineralization: How Many Amorphous Calcium Carbonates Are There?

Although the polymorphism of calcium carbonate is well known, and its polymorphs-calcite, aragonite, and vaterite-have been highly studied in the context of biomineralization, polyamorphism is a much more recently discovered phenomenon, and the existence of more than one amorphous phase of calcium carbonate in biominerals has only very recently been understood. Here we summarize what is known about polyamorphism in calcium carbonate as well as what is under- stood about the role of amorphous calcium carbonate in biominerals. We show that consideration of the amorphous forms of calcium carbonate within the physical notion of polyamorphism leads to new insights when it comes to the mechanisms by which polymorphic structures can evolve in the first place. This not only has implications for our understanding of biomineralization, but also of the means by which crystallization may be controlled in medical, pharmaceutical, and industrial contexts.

cond-mat.mtrl-sci↗

arXiv2012

Reactive Force Field for Proton Diffusion in BaZrO3 using an empirical valence bond approach

A new reactive force field to describe proton diffusion within the solid-oxide fuel cell material BaZrO3 has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO3 have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.

cond-mat.mtrl-sci↗

arXiv2001

Two distinct metallic bands associated with monatomic Au wires on the Si(557)-Au surface

The Si(557)-Au surface, containing monatomic Au wires parallel to the steps, has been proposed as an experimental realization of an ideal one-dimensional metal. In fact, recent photoemission experiments on this system (Nature 402, 504 (1999)) found two peaks that were interpreted in terms of the spin-charge separation in a Luttinger liquid. Our first-principles density functional calculations reveal two metallic bands associated with Au-Si bonds, instead of the single band expected from the Au 6s states, providing an alternative explanation for the experimental observations.

cond-mat.mtrl-sci↗

arXiv2001

Efficient index handling of multidimensional periodic boundary conditions

An efficient method is described to handle mesh indexes in multidimensional problems like numerical integration of partial differential equations, lattice model simulations, and determination of atomic neighbor lists. By creating an extended mesh, beyond the periodic unit cell, the stride in memory between equivalent pairs of mesh points is independent of their position within the cell. This allows to contract the mesh indexes of all dimensions into a single index, avoiding modulo and other implicit index operations.

cond-mat.mtrl-sci↗