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Comparison between solid- and solution-state intermolecular interactions identify solvent-dependant pathways directing crystallisation into different polymorphic forms.

We report the effects of radiation damage on helium diffusion in zircon using data from molecular dynamics simulations. We observe an increase in activation energy for helium diffusion as a result of radiation damage and increasing structural disorder. The activation energy in a heavily damaged region is smaller than in a completely amorphous system which is correlated with remaining order in the cation sublattices of the damaged structure not present in the fully amorphized system. The increase in activation energy is related to the disappearance of fast diffusion pathways that are present in the crystal. Consistent with the change in activation energy, we observe the accumulation of helium atoms in the damaged structure and discuss the implications of this effect for the formation of helium bubbles and zircon’s performance as an encapsulation material for nuclear waste. Graphic abstract

In the late 1970s, the embryonic UK research community in molecular simulation – physicists and physical chemists – organised itself around CCP5, one of a set of Collaborative Computational Projects in different fields. CCP5 acted to develop and use the software required by an evolving and expanding scientific agenda, to exploit quickly and efficiently the revolution in computing hardware and to educate and nurture the careers of future generations of researchers in the field. This collaboration formally began in 1980, and is still fully active now, 40 years later. Today, molecular simulation techniques, many of them pioneered by CCP5, are now used very widely, including in several other CCPs in the UK’s current family of Collaborative Computational Projects. This article tells the story of molecular simulation in the UK, with CCP5 itself at centre stage, using the written records in the CCP archives. The authors were, or are, all personally involved in this story.

Polyproline II (pPII) is a left-handed 31-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and β-sheet. Although pPII has been reported as the most stable conformation for several unfolded short chain peptides in aqueous solution, it is rarely observed in their solid state. Here, we show for the first time a glycine homopeptide (gly-gly-gly) adopting the pPII conformation in its crystalline dihydrate structure. The single crystal X-ray structure with molecular dynamic simulation suggests that a network of water and the charged carboxylate group is critical in stabilizing the pPII conformation in solid state, offering an insight into the structures of unfolded regions of proteins and the role of water in peptide crystallization.

We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging Brownian quasiparticles arise naturally from its geometric definition and include both conservative repulsion and dissipative drag forces. The quasiparticles, which are composed of atomistic host solvent rather than being simply immersed in it, provide a link between the atomistic and DPD levels and a practical route to extract the DPD parameters as direct statistical averages over the atomistic host system. The method thus provides the molecular foundations for the mesoscopic DPD. It is illustrated on the example of simple monatomic supercritical fluid demonstrating good agreement in thermodynamic and transport properties calculated for the atomistic system and DPD using the obtained parameters., Comment: 13 pages, 5 figures. Contribution to the DL_POLY 25th Anniversary Special Meeting, 3-4 Nov 2017, Chichely Hall, MK16 9JJ, UK

Three separately developed software Molecular Dynamics packages at Daresbury Laboratory, namely DL_FIELD (DL_F), DL_POLY and DL_ANALYSER, have been integrated to form an efficient computational inf...

Software citation contributes to achieving software sustainability in two ways: It provides an impact metric to incentivize stakeholders to make software sustainable. It also provides references to software used in research, which can be reused and adapted to become sustainable. While software citation faces a host of technical and social challenges, community initiatives have defined the principles of software citation and are working on implementing solutions., 2 pages; accepted by ICSE 2021 BokSS Workshop (https://bokss.github.io/bokss2021/)

Pragmatic interoperability between platforms and service-oriented architectures exists whenever there is an agreement on the roles of participants and components as well as minimum standards for good practice. In this work, it is argued that open platforms require pragmatic interoperability, complementing syntactic interoperability (e.g., through common file formats), and semantic interoperability by ontologies that provide agreed definitions for entities and relations. For consistent data management and the provision of services in computational molecular engineering, community-governed agreements on pragmatics need to be established and formalized. For this purpose, if ontology-based semantic interoperability is already present, the same ontologies can be used. This is illustrated here by the role of the “translator” and procedural definitions for the process of “translation” in materials modelling, which refers to mapping industrial research and development problems onto solutions by modelling and simulation. For associated roles and processes, substantial previous standardization efforts have been carried out by the European Materials Modelling Council (EMMC ASBL). In the present work, the Materials Modelling Translation Ontology (MMTO) is introduced, and it is discussed how the MMTO can contribute to formalizing the pragmatic interoperability standards developed by EMMC ASBL.

The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.

We report the results of a large-scale modelling study of radiation damage effects in the nuclear waste form zirconolite. We particularly focus on the effects of radiation damage in amorphous zirconolite and have developed a new way to analyse the damaged structure in terms of local coordination statistics. On the basis of this analysis, we find that the amorphous structure responds to radiation damage differently from the crystal. Amorphous zirconolite is found to be “softer” than crystalline zirconolite with a much larger number of atoms becoming displaced and changing coordination during a 70 keV cascade. The local coordination and connectivity analysis shows that the amorphous structure continues to evolve as a result of repeated radiation damage, changes which cannot be identified from globally averaged properties such as pair distribution functions. We also find large density inhomogeneities at the local level which we suggest may play an important role for future developments in nuclear waste storage. Finally, we find a correlation between the changes in enthalpy and local coordination, suggesting that measurements of enthalpy change can be linked quantitatively to structural radiation damage. Our results raise an interesting possibility of whether an evolution of the amorphous structure due to radiation damage can converge to a new equilibrium amorphous regime, posing the fundamental question of what that structure may be.

Including the effects of excited electrons in classical simulations, at the level of the two-temperature model, involves the coupling of a grid-based finite-difference solver for a heat diffusion e...

It was my pleasure to organise and celebrate the 25th anniversary of the DL_POLY project as a special event at the Royal Society’s Chicheley Hall in November 2017. This special issue of Molecular S...

We report a study of the absorption of CO2 into a number of zinc imidazolate framework structures, and subsequent desorption, using the molecular dynamics simulation method with force fields partly developed by ourselves. The simulations primarily give results concerning the mechanism of CO2 absorption under conditions likely to be found in industrial waste gas streams. In particular we compare the rate of uptake of CO2 for different ZIFs. We also show that it is possible to observe desorption by reduced pressure and high temperature. These characteristics confirm that ZIFs might be suitable for CO2 absorption within an industrial capture and sequestration process.

The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO) is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of data and metadata at the VIMMP marketplace frontend., The Virtual Materials Marketplace (VIMMP) project is funded from the European Union's Horizon 2020 research and innovation programme under grant agreement no. 760907

The nature of the amorphous state has been notably difficult to ascertain at the microscopic level. In addition to the fundamental importance of understanding the amorphous state, potential changes to amorphous structures as a result of radiation damage have direct implications for the pressing problem of nuclear waste encapsulation. Here, we develop new methods to identify and quantify the damage produced by high-energy collision cascades that are applicable to amorphous structures and perform large-scale molecular dynamics simulations of high-energy collision cascades in a model zircon system. We find that, whereas the averaged probes of order such as pair distribution function do not indicate structural changes, local coordination analysis shows that the amorphous structure substantially evolves due to radiation damage. Our analysis shows a correlation between the local structural changes and enthalpy. Important implications for the long-term storage of nuclear waste follow from our detection of significant local density inhomogeneities. Although we do not reach the point of convergence where the changes of the amorphous structure saturate, our results imply that the nature of this new converged amorphous state will be of substantial interest in future experimental and modelling work., Comment: 11 pages, 15 figures

Large-scale molecular dynamics simulations have been used to study the microstructure in Y-doped ${\mathrm{ZrO}}_{2}$. From simulations performed as a function of composition the dependence of microstructure on composition is quantified, showing how it is formed from two coexisting phases, and the transformation to the stabilized cubic form is observed at higher concentrations of yttrium and higher temperatures. The effect of composition and temperature on oxygen diffusion is also studied, showing strong correlations between microstructure and diffusion.

The accuracy and robustness of new Buckingham potentials for the pyrochlores Gd2Ti2O7 and Gd2Zr2O7 is demonstrated by calculating and comparing values for a selection of point defects with those calculated using a selection of other published potentials and our own ab inito values. Frenkel pair defect formation energies are substantially lowered in the presence of a small amount of local cation disorder. The activation energy for oxygen vacancy migration between adjacent O48f sites is calculated for Ti and Zr pyrochlores with the energy found to be lower for the non-defective Ti than for the Zr pyrochlore by ∼0.1 eV. The effect of local cation disorder on the VO48f → VO48f migration energy is minimal for Gd2Ti2O7, while the migration energy is lowered typically by ∼43 % for Gd2Zr2O7. As the healing mechanisms of these pyrochlores are likely to rely upon the availability of oxygen vacancies, the healing of a defective Zr pyrochlore is predicted to be faster than for the equivalent Ti pyrochlore.

© 2016 American Chemical Society. Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

Halothane binding to hydrated dimyristoylphosphatidylcholine (DMPC) bilayer membranes has been examined over a wide range of pressures from 105 to 4 × 108 Pa. We show that the solvation of halothane by the membrane and bulk water are both pressure dependent, with an increased pressure driving halothane into the membrane. Analysis of these results shows that this pressure dependence is not the cause of pressure reversal, the process whereby general anaesthetics lose their efficacy at pressures of about 8 × 106 to about 2.5 × 107 Pa.

A suite of application benchmarks, designed to be broadly representative of UK HPC usage, has been developed to stress a broad range of architectural features of large scale parallel HPC resources. A generic methodology to investigate application performance and scaling characteristics has been defined, resulting in a detailed understanding of the performance of these applications. This methodology is transferable to other applications and systems: it is of practical value to developers and users who are aiming for optimal utilisation of HPC resources. An understanding of the performance characteristics of a range of large-scale HPC resources has been obtained using low-level synthetic benchmarks. A relatively simple, qualitative mechanism to assess and predict application performance on current and future architectures using synthetic benchmark results together with application performance analysis results is explored.

A molecular dynamics (MD) study of MgxAlyOz thin films grown by magnetron sputtering is presented using an ionic model and comparing two potential sets with formal and partial charges. The applicability of the model and the reliability of the potential sets for the simulation of thin film growth are discussed. The formal charge potential set was found to reproduce the thin film structure in close agreement with the structure of the experimentally grown thin films. Graphical abstract A molecular dynamics study of growth of MgxAlyOz thin films is presented using an ionic model and comparing two potential sets with formal and partial charges. The simulation results with the formal charge potential set showed a transition in the film from a crystalline to an amorphous structure, when the Mg metal content decreases below 50% in very close agreement with the structure of the experimentally deposited films.

We review the work carried out within the e Minerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

DL_POLY_3 is a general purpose molecular dynamics (MD) simulation package designed to simulate systems of the order of tens of millions of particles and beyond by efficiently harnessing the power of modern computer clusters. Here we discuss the package design, functionality and report on performance and capability limits. We then report the application of DL_POLY_3 to study radiation cascades in Gd2Ti2O7 and Gd2Zr2O7, potential materials for high-level radioactive waste storage and discuss problems associated with the analysis of the cascades. We see little direct amorphisation but rather the start of a transition to the fluorite structure which is more pronounced for the Zr than the Ti compound.

Recently, there has been a concerted effort to implement advanced classical potential energy surfaces by adding higher order multipoles to fixed point charge electrostatics in a bid to increase the accuracy of simulations of condensed phase systems. One major hurdle is the unwieldy nature of the expressions which in part has limited developers mostly to including only dipoles and quadrupoles. In this paper, we present a generalization of the Cartesian formulation of electrostatic multipolar interactions that enables the specification of an arbitrary order of multipoles. Specifically, we derive formulas for arbitrary order implementation of the particle mesh Ewald method and give a closed form formula for the stress tensor in the reciprocal space. In addition, we provide recurrence relations for common electrostatic potentials employed in molecular simulations, which allows for the generalization to arbitrary order and guarantees a computational cost that scales as O(p(3)) for Cartesian multipole interactions of order p.

We discuss how structural disorder and amorphization affects solid-state diffusion, and consider zirconolite as a currently important case study. By performing extensive molecular dynamics simulations, we disentangle the effects of amorphization and density, and show that a profound increase of solid-state diffusion takes place as a result of amorphization. Importantly, this can take place at the same density as in the crystal, representing an interesting general insight regarding solid-state diffusion. We find that decreasing the density in the amorphous system increases pre-factors of diffusion constants, but not decreasing the activation energy. We also find that atomic species in zirconolite are affected differently by amorphization and density change. Our microscopic insights are relevant for understanding how solid-state diffusion changes due to disorder and for building predictive models of operation of materials to be used to encapsulate nuclear waste.

We use the example of a study of the compressibility anomaly in amorphous silica to illustrate how molecular-scale simulations can be performed using grid computing. The potential for running many simulations within a single study requires the use of new data management methods, which are discussed in this paper. The example of silica highlights the advantages of the use of grid computing for studying subtle effects.