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2. Fast, accurate, and transferable many-body interatomic potentials by symbolic regression

Author

Hernandez, Alberto, Balasubramanian, Adarsh, Yuan, Fenglin, Mason, Simon, and Mueller, Tim

Subjects
Physics - Computational Physics, Condensed Matter - Materials Science, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Machine Learning, Computer Science - Neural and Evolutionary Computing
Abstract

The length and time scales of atomistic simulations are limited by the computational cost of the methods used to predict material properties. In recent years there has been great progress in the use of machine learning algorithms to develop fast and accurate interatomic potential models, but it remains a challenge to develop models that generalize well and are fast enough to be used at extreme time and length scales. To address this challenge, we have developed a machine learning algorithm based on symbolic regression in the form of genetic programming that is capable of discovering accurate, computationally efficient manybody potential models. The key to our approach is to explore a hypothesis space of models based on fundamental physical principles and select models within this hypothesis space based on their accuracy, speed, and simplicity. The focus on simplicity reduces the risk of overfitting the training data and increases the chances of discovering a model that generalizes well. Our algorithm was validated by rediscovering an exact Lennard-Jones potential and a Sutton Chen embedded atom method potential from training data generated using these models. By using training data generated from density functional theory calculations, we found potential models for elemental copper that are simple, as fast as embedded atom models, and capable of accurately predicting properties outside of their training set. Our approach requires relatively small sets of training data, making it possible to generate training data using highly accurate methods at a reasonable computational cost. We present our approach, the forms of the discovered models, and assessments of their transferability, accuracy and speed.

Published
2019

38. Co‐expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes.

Author

Barratt, Liam J., He, Zhesi, Fellgett, Alison, Wang, Lihong, Mason, Simon McQueen, Bancroft, Ian, and Harper, Andrea L.

Subjects
REGULATOR genes, GENE expression, GENETIC variation, CROP yields, CROP growth, WHEAT, GENE regulatory networks
Abstract

SUMMARY: Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co‐expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat‐shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master‐regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat‐stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression – presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate‐resilient crops. Significance Statement: Global wheat yields and crop growth are vulnerable to damage by heat stress, a threat that is likely to become more common globally in the coming years through climate change. Conducting weighted co‐expression network analysis on 337 diverse landrace accessions, we identified and validated TraesCS4D01G207500.1 as a hub gene that can be used as a marker of early thermotolerance, seemingly via the regulation of the expression of a suite of HSP and HSF genes. [ABSTRACT FROM AUTHOR]

Published
2023
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39. Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans

Author

Besser, Katrin, Malyon, Graham P., Eborall, William S., Paro da Cunha, Giovanni, Filgueiras, Jefferson G., Dowle, Adam, Cruz Garcia, Lourdes, Page, Samuel J., Dupree, Ray, Kern, Marcelo, Gomez, Leonardo D., Li, Yi, Elias, Luisa, Sabbadin, Federico, Mohamad, Shaza E., Pesante, Giovanna, Steele-King, Clare, Ribeiro de Azevedo, Eduardo, Polikarpov, Igor, Dupree, Paul, Cragg, Simon M., Bruce, Neil C., and McQueen-Mason, Simon J.

Published
2018
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40. The synthesis and reactivity of four- and five-membered metallacycles of platinum and palladium

Author

Mason, Simon

Subjects
540
Abstract

Chapter 1 reviews the literature concerning the synthesis and reactivity of oxodimethyl- enemethane metal complexes and their applications in organic synthesis. The preparation of metal-ureylene complexes and amino acid complexes of platinum are also discussed. Chapter 2 describes the synthesis of metallaphosphetane-3-oxide complexes of platinum and palladium, [M {CH(R)P(O)(Ph)CHR} L2]. Crystallographic and n.m.r. evidence for benzoyl substituted complexes, indicates that the four-membered rings are puckered, with the phosphoryl oxygen adopting an equatorial environment. The ligand substitution reactions of platinum analogues are also discussed. The preparation of new platina-2,4,3-diazaphosphetidine-3-oxide complexes, [Pt{N(R)P(O)(Ph)NR}L2] is presented in Chapter 3. An X-ray crystal structure determination on an N,N -diphenyl derivative indicates that the four-membered metalla-cyclic ring is almost planar, the nitrogen atoms of which show sp2 hybrid character. An investigation into the insertion reactions of the N,N'-dihydrogen derivatives with dimethyl acetylenedicarboxylate resulted in the isolation of six-membered platinacyclic products, characterised by n.m.r. and i.r. spectroscopy. Attempts to prepare a similar insertion product using hexafluorobut-2-yne, led only to the formation of an organic polymeric material. The formation of a novel four-membered ring species containing a phosphin-imine functionality [Pt{SP(=NPh)(Ph)NPh}L2] is also described in Chapter 3. The phos-phinimine group was shown to have Lewis base capabilities and also underwent Wittig-type reactions with C=O and C=S containing molecules to form [Pt{SP(O)(Ph)NPh}L2] and [Pt{SP(S)(Ph)S)L2] ring systems respectively. The formation and characterisation of phosphonato, phosphato and arsonato complexes of platinum(II) are described in Chapter 4. The molecular structure of a bis(phosphine)phos- phonato complex establishes the presence of a slightly puckered four-membered ring with the phosphoryl oxygen adopting an equatorial position. The decomposition in solution of a bis(benzyldiphenylphosphine) analogue led to the formation of the di-orthometallated product cis-[Pt{C6H4CH2PPh2}2], as shown by X-ray crystallography. Chapter 5 describes the synthesis of five-membered platinacycles containing amino acid derivatives, [Pt{N(R2)-CH(R1)-C(O)O}L2]. An X-ray crystal structure determination on an [N-acetylglycinato(2-)-N,O] complex, indicated the presence of an almost planar five- membered ring that contains substantial electron delocalisation within the carboxylate and amide functionalities. The reaction of these complexes in ethanol with carbon monoxide or sulphur dioxide led to the formation of bis(ethoxycarbonyl) or bis(ethylsulphonato) metal complexes respectively. The final Chapter investigates the syntheses of several new five-membered metallacyclic species which contain metal bonds to carbon, nitrogen, oxygen or sulphur. The isolation of the metallaoxacyclopentenone ring system [Pt{CH=C(NHCOMe)C(O)O}L2], formed via the rearrangement of an initially produced [Pt{N(COMe)C(=CH2)C(O)O}L2] species, was confirmed by a single crystal X-ray diffraction study. The natures of the other complexes were examined using n.m.r. and i.r. spectroscopy.

Published
1991

42. Flexible forecast presentation overcomes longstanding obstacles to using probabilistic seasonal forecasts

Author

Hansen, James W., Dinku, Tufa, Robertson, Andrew W., Cousin, Remi, Trzaska, Sylwia, and Mason, Simon J.

Subjects
Atmospheric Science, Global and Planetary Change, Management, Monitoring, Policy and Law, Environmental Science (miscellaneous), Pollution
Abstract

We describe an innovative forecast presentation that aims to overcome obstacles to using seasonal climate forecasts for decision making, trace factors that influenced how seasonal forecast conventions have evolved, and describe a workshop process for training and supporting farmers in sub-Saharan Africa to use probabilistic seasonal forecasts. Mainstreaming seasonal climate forecasts through Regional Climate Outlook Forums (RCOFs) was an important milestone in the development of climate services. Most RCOFs and National Meteorological Services (NMS) adopted a subjective process to arrive at a consensus among different sources of prediction, and express the forecast as probabilities that rainfall in the upcoming season will fall in “below-normal,” “normal” or “above-normal” historical tercile categories. The Flexible Forecast is an online presentation that rectifies the main criticisms of the tercile convention by presenting downscaled forecasts as full probability distributions in probability-of-exceedance format along with the historical climate distribution. A map view provides seasonal forecast quantities, anomalies, or probabilities of experiencing above or below a user-selected threshold in amount or percentile, at the spatial resolution of the underlying gridded data (typically 4 to 5 km). We discuss factors that contributed to the persistence of the tercile convention, and milestones that paved the way to adopting seasonal forecast methods and formats that better align with user needs. The experience of adopting the new flexible forecast presentation regionally and at a national level in Eastern Africa illustrates the challenges and how they can be overcome. We also describe a seasonal forecast training and planning workshop process that has been piloted with smallholder farmers in several African countries. Beginning with participants' collective memory of past seasonal climate variations, the process leads them incrementally to understand the forecast presented in probability-of-exceedance format, and apply it to their seasonal planning decisions.

Published
2022

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