scholarly journals Machine learning potentials for extended systems: a perspective

2021 ◽  
Vol 94 (7) ◽  
Author(s):  
Jörg Behler ◽  
Gábor Csányi

Abstract In the past two and a half decades machine learning potentials have evolved from a special purpose solution to a broadly applicable tool for large-scale atomistic simulations. By combining the efficiency of empirical potentials and force fields with an accuracy close to first-principles calculations they now enable computer simulations of a wide range of molecules and materials. In this perspective, we summarize the present status of these new types of models for extended systems, which are increasingly used for materials modelling. There are several approaches, but they all have in common that they exploit the locality of atomic properties in some form. Long-range interactions, most prominently electrostatic interactions, can also be included even for systems in which non-local charge transfer leads to an electronic structure that depends globally on all atomic positions. Remaining challenges and limitations of current approaches are discussed. Graphic Abstract

Author(s):  
Emir Kocer ◽  
Tsz Wai Ko ◽  
Jörg Behler

In the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Sungmin O. ◽  
Rene Orth

AbstractWhile soil moisture information is essential for a wide range of hydrologic and climate applications, spatially-continuous soil moisture data is only available from satellite observations or model simulations. Here we present a global, long-term dataset of soil moisture derived through machine learning trained with in-situ measurements, SoMo.ml. We train a Long Short-Term Memory (LSTM) model to extrapolate daily soil moisture dynamics in space and in time, based on in-situ data collected from more than 1,000 stations across the globe. SoMo.ml provides multi-layer soil moisture data (0–10 cm, 10–30 cm, and 30–50 cm) at 0.25° spatial and daily temporal resolution over the period 2000–2019. The performance of the resulting dataset is evaluated through cross validation and inter-comparison with existing soil moisture datasets. SoMo.ml performs especially well in terms of temporal dynamics, making it particularly useful for applications requiring time-varying soil moisture, such as anomaly detection and memory analyses. SoMo.ml complements the existing suite of modelled and satellite-based datasets given its distinct derivation, to support large-scale hydrological, meteorological, and ecological analyses.


Nanoscale ◽  
2021 ◽  
Author(s):  
Daniele Dragoni ◽  
Jörg Behler ◽  
Marco Bernasconi

Large scale atomistic simulations with an interatomic potential generated by a machine learning method have been exploited to study the crystallization of Sb in ultrathin films.


2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Sebastian Spänig ◽  
Siba Mohsen ◽  
Georges Hattab ◽  
Anne-Christin Hauschild ◽  
Dominik Heider

Abstract Owing to the great variety of distinct peptide encodings, working on a biomedical classification task at hand is challenging. Researchers have to determine encodings capable to represent underlying patterns as numerical input for the subsequent machine learning. A general guideline is lacking in the literature, thus, we present here the first large-scale comprehensive study to investigate the performance of a wide range of encodings on multiple datasets from different biomedical domains. For the sake of completeness, we added additional sequence- and structure-based encodings. In particular, we collected 50 biomedical datasets and defined a fixed parameter space for 48 encoding groups, leading to a total of 397 700 encoded datasets. Our results demonstrate that none of the encodings are superior for all biomedical domains. Nevertheless, some encodings often outperform others, thus reducing the initial encoding selection substantially. Our work offers researchers to objectively compare novel encodings to the state of the art. Our findings pave the way for a more sophisticated encoding optimization, for example, as part of automated machine learning pipelines. The work presented here is implemented as a large-scale, end-to-end workflow designed for easy reproducibility and extensibility. All standardized datasets and results are available for download to comply with FAIR standards.


2020 ◽  
Author(s):  
Rene Orth ◽  
Sungmin Oh

<p>Soil moisture plays a key role in land-atmosphere interactions through its influence on the energy and water cycles. Furthermore, its spatiotemporal variations can affect the development and persistence of extreme weather events. Consequently, soil moisture information is required for a wide range of research and applications, such as agricultural monitoring, flood and drought prediction, climate projection, and carbon-cycle modeling. Despite its scientific and societal importance, observations of soil moisture are sparse, in particular across time and at large spatial scales. Only models and satellite retrievals can provide global soil moisture information. While the ability of land surface models to represent the complex land-atmosphere interplay is still limited, satellite-based soil moisture data are a valuable alternative. However, these products suffer from a scaling based on models, and can only capture the top few centimeters of the soil. </p><p>In this study, we aim to augment satellite-based soil moisture data using machine learning. For this purpose we integrate satellite soil moisture with multiple hydro-meteorological data streams to derive global gridded soil moisture using Long Short-Term Memory (LSTM) neural networks. These networks are trained using in-situ soil moisture measurements as target data. With the resulting self-learned relationships, the LSTMs can produce in-situ-like soil moisture globally. We further analyze the implications of using point-scale target data to infer large scale information. The new dataset is derived separately for the surface and the deeper soil, thereby extending beyond the range covered by the satellite-based products. The integration of many data streams and multiple soil moisture observations through a powerful synergistic technique offers the potential to yield high accuracy. This is tested through rigorous cross-validation of the derived dataset. Finally, the planned datasets will permit consistent long-term, large-scale analysis to enhance our understanding of the hydrology-biosphere-climate interplay, to better constrain models and to support hydrological hazards monitoring and climate projections.</p>


2021 ◽  
pp. 095400832110171
Author(s):  
Cheng Wang ◽  
Long Fei Zhang ◽  
Wa Li ◽  
Li Rong Yang ◽  
Jia Jun Ma ◽  
...  

Aromatic thermoset materials have shown great potential applications in various fields owing to their excellent mechanical strengths. However, their poor ductility is still hinders their large-scale applications. In this study, a new class of aromatic thermosets consisting of two types of crosslinks was successfully developed by incorporating the special group imidazole into a type of crosslinked thermoset. One crosslink is constituted of reversible multiple noncovalent interactions containing “face-face” π–π stacking, “point-point” hydrogen bonds, and ion-pair electrostatic interactions, whereas the other is composed of permanent covalent bonds. Most importantly, the synergetic interplay among these reversible multiple noncovalent interactions enables them to evade the restrictions from the aromatic polymer skeletons to proceed with their dynamic dissociating-rebuilding processes, which can timely and effectively dissipate the internal stress. Finally, owing to the coefficient of these two types of crosslinks, a significantly enhanced ductility was successfully obtained on these aromatic thermosets and their tensile strengths were also improved. Such thermosets having simultaneously enhanced strengths and ductility are predicted to be eventually used in a wide range of applications.


Catalysts ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1001
Author(s):  
Heesoo Park ◽  
El Tayeb Bentria ◽  
Sami Rtimi ◽  
Abdelilah Arredouani ◽  
Halima Bensmail ◽  
...  

Nowadays, most experiments to synthesize and test photocatalytic antimicrobial materials are based on trial and error. More often than not, the mechanism of action of the antimicrobial activity is unknown for a large spectrum of microorganisms. Here, we propose a scheme to speed up the design and optimization of photocatalytic antimicrobial surfaces tailored to give a balanced production of reactive oxygen species (ROS) upon illumination. Using an experiment-to-machine-learning scheme applied to a limited experimental dataset, we built a model that can predict the photocatalytic activity of materials for antimicrobial applications over a wide range of material compositions. This machine-learning-assisted strategy offers the opportunity to reduce the cost, labor, time, and precursors consumed during experiments that are based on trial and error. Our strategy may significantly accelerate the large-scale deployment of photocatalysts as a promising route to mitigate fomite transmission of pathogens (bacteria, viruses, fungi) in hospital settings and public places.


1995 ◽  
Vol 283 ◽  
pp. 43-95 ◽  
Author(s):  
P. K. Yeung ◽  
James G. Brasseur ◽  
Qunzhen Wang

As discussed in a recent paper by Brasseur & Wei (1994), scale interactions in fully developed turbulence are of two basic types in the Fourier-spectral view. The cascade of energy from large to small scales is embedded within ‘local-to-non-local’ triadic interactions separated in scale by a decade or less. ‘Distant’ triadic interactions between widely disparate scales transfer negligible energy between the largest and smallest scales, but directly modify the structure of the smallest scales in relationship to the structure of the energy-dominated large scales. Whereas cascading interactions tend to isotropize the small scales as energy moves through spectral shells from low to high wavenumbers, distant interactions redistribute energy within spectral shells in a manner that leads to anisotropic redistributions of small-scale energy and phase in response to anisotropic structure in the large scales. To study the role of long-range interactions in small-scale dynamics, Yeung & Brasseur (1991) carried out a numerical experiment in which the marginally distant triads were purposely stimulated through a coherent narrow-band anisotropic forcing at the large scales readily interpretable in both the Fourier- and physical-space views. It was found that, after one eddy turnover time, the smallest scales rapidly became anisotropic as a direct consequence of the marginally distant triadic group in a manner consistent with the distant triadic equations. Because these asymptotic equations apply in the infinite Reynolds number limit, Yeung & Brasseur argued that the observed long-range effects should be applicable also at high Reynolds numbers.We continue the analysis of forced simulations in this study, focusing (i) on the detailed three-dimensional restructuring of the small scales as predicted by the asymptotic triadic equations, and (ii) on the relationship between Fourier- and physical-space evolution during forcing. We show that the three-dimensional restructuring of small-scale energy and vorticity in Fourier space from large-scale forcing is predicted in some detail by the distant triadic equations. We find that during forcing the distant interactions alter small-scale structure in two ways: energy is redistributed anisotropically within high-wavenumber spectral shells, and phase correlations are established at the small scales by the distant interactions. In the numerical experiments, the long-range interactions create two pairs of localized volumes of concentrated energy in three-dimensional Fourier space at high wavenumbers in which the Fourier modes are phase coupled. Each pair of locally phase-correlated volumes of Fourier modes separately corresponds to aligned vortex tubes in physical space in two orthogonal directions. We show that the dynamics of distant interactions in creating small-scale anisotropy may be described in physical space by differential advection and distortion of small-scale vorticity by the coherent large-scale energy-containing eddies, producing anisotropic alignment of small-scale vortex tubes.Scaling arguments indicate a disparity in timescale between distant triadic interactions and energy-cascading local-to-non-local interactions which increases with scale separation. Consequently, the small scales respond to forcing initially through the distant interactions. However, as energy cascades from the large-scale to the small-scale Fourier modes, the stimulated distant interactions become embedded within a sea of local-to-non-local energy cascading interactions which reduce (but do not eliminate) small-scale anisotropy at later times. We find that whereas the small-scale structure is still anisotropic at these later times, the second-order velocity moment tensor is insensitive to this anisotropy. Third-order moments, on the other hand, do detect the anisotropy. We conclude that whereas a single statistical measure of anisotropy can be used to indicate the presence of anisotropy, a null result in that measure does not necessarily imply that the signal is isotropic. The results indicate that non-equilibrium non-stationary turbulence is particularly sensitive to long-range interactions and deviations from local isotropy.


Author(s):  
A. Brad Murray ◽  
Andrew D. Ashton

Recent research addresses the formation of patterns on sandy coastlines on alongshore scales that are large compared with the cross-shore extent of active sediment transport. A simple morphodynamic instability arises from the feedback between wave-driven alongshore sediment flux and coastline shape. Coastline segments with different orientations experience different alongshore sediment fluxes, so that curvatures in coastline shape drive gradients in sediment flux, which can augment the shoreline curvatures. In a simple numerical model, this instability, and subsequent finite-amplitude interactions between pattern elements, lead to a wide range of different rhythmic shapes and behaviours—ranging from symmetric cuspate capes and bays to alongshore migrating ‘flying spits’—depending on the characteristics of the input wave forcing. The scale of the pattern coarsens in some cases because of the merger of migrating coastline features, and in other cases because of non-local screening interactions between coastline protrusions, which affect the waves reaching other parts of the coastline. Features growing on opposite sides of an enclosed water body mutually affect the waves reaching each other in ways that lead to the segmentation of elongated water bodies. Initial tests of model predictions and comparison with observations suggest that modes of pattern formation in the model are relevant in nature.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yury Lysogorskiy ◽  
Cas van der Oord ◽  
Anton Bochkarev ◽  
Sarath Menon ◽  
Matteo Rinaldi ◽  
...  

AbstractThe atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code that is suitable for use in large-scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in shifts a previously established Pareto front for machine learning interatomic potentials toward faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.


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