Mellora de métodos computacionais semiempíricos para a predición de reactividade química mediante técnicas de “machine learning”

Traballo Fin de Grao en Química. Curso 2020-2021O machine learning e a intelixencia artificial estanse convertindo en técnicas cada vez máis presentes na investigación en química computacional. A medida que temos acceso a unha maior cantidade datos de química cuántica, aumentan as posibilidades de uso de algoritmos intelixentes para a exploración do espazo químico. Por outra parte, aínda non dispoñemos de métodos eficientes para a predición de propiedades de reacción cuantitativas. Entre estas propiedades atópase a enerxía de activación, cuxa predición de forma precisa proporcionaría un método para o descubrimento de novos mecanismos de reacción e forneceríanos control sobre a cinética das reaccións. O presente traballo intenta buscar un algoritmo baseado en machine learning para a predición de enerxías de activación. O noso modelo depende dun cálculo a nivel semiempírico (PM7) e proporciona unha predición a nivel DFT mediante machine learning. Con este procedemento, conseguimos precisión química cun custo computacional reducido. Ademais de obter un rendemento equiparable ao estado da arte, esta alternativa contribúe con descritores personalizados, que poden ser incorporados en novos procedementos de minaría de datos na química. Por último, tamén proporciona unha interpretación do modelo dende a perspectiva da intuición química.El machine learning y la inteligencia artificial se están convirtiendo en técnicas cada vez más presentes en la investigación en química computacional. A medida que tenemos acceso a una mayor cantidad de datos de química cuántica, aumentan las posiblidades de uso de algoritmos inteligentes para la exploración del espacio químico. Por otra parte, todavía no disponemos de métodos eficientes para la predicción de propiedades de reacción cuantitativas. Entre estas propiedades se encuentra la energía de activación, cuya predicción de forma precisa proporcionaría un método para el descubrimiento de nuevos mecanismos de reacción y nos facilitaría el control sobre la cinética de las reacciones. El presente trabajo intenta buscar un algoritmo basado en machine learning para la predicción de energías de activación. Nuestro modelo depende de un cálculo a nivel semiempírico (PM7) y proporciona una predicción a nivel DFT mediante machine learning. Con este procedimiento, conseguimos precisión química con un coste computacional reducido. Además de obtener un rendimiento equiparable al estado del arte, esta alternativa contribuye con descriptores personalizados, que pueden ser incorporados en procedimientos de minería de datos en la química. Por último, también proporciona una interpretación del modelo desde una perspectiva de la intuición química.Machine learning and artificial intelligence are becoming ubiquitous techniques in computational chemistry research. With quantum-chemical data becoming increasingly available, intelligent algorithms are taking the upper hand in the exploration of the chemical space. On the other hand, we still lack efficient algorithms when it comes to predicting quantitative reaction properties. Within this properties, accurately predicting activation energies would enable rapid discovery of new reaction mechanisms and would grant control over chemical kinetics. The present work intends to seek for a machine learning-based algorithm to predict activation energies. Our model relies on a semiempirical calculation (PM7 level of theory) and resorts to machine learning to DFT accuracy. With this procedure, we can obtain chemical accuracy while limiting the computational expenditure. In addition to achieving state of the art performance, this approach contribute with innovative custom descriptors that can be harnessed in data mining techniques in the chemical domain and allow interpretability from the perspective of chemical intuition

Barrier height prediction by machine learning correction of semiempirical calculations

Different machine learning (ML) models are proposed in the present work to predict DFT-quality barrier heights (BHs) from semiempirical quantum-mechanical (SQM) calculations. The ML models include multi-task deep neural network, gradient boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute errors (MAEs) are similar or slightly better than previous models considering the same number of data points. Unlike other ML models employed to predict BHs, entropic effects are included, which enables the prediction of rate constants at different temperatures. The ML corrections proposed in this paper could be useful for rapid screening of the large reaction networks that appear in Combustion Chemistry or in Astrochemistry. Finally, our results show that 70% of the bespoke predictors are amongst the features with the highest impact on model output. This custom-made set of predictors could be employed by future delta-ML models to improve the quantitative prediction of other reaction properties

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Borophene vs. graphene interfaces: Tuning the electric double layer in ionic liquids

Producción CientíficaIn this work we perform molecular dynamics simulations of mixtures of a prototypical protic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), with lithium tetrafluoroborate (LiBF4), confined between two borophene walls of three different surface charges, −1, 0 and +1 e/nm2, where e is the elementary charge. The properties of the system are analyzed by means of ionic density profiles, angular orientations of [BMIM]+ cations close to the wall and vibrational densities of states for the salt cations close to the walls. The lateral structure of the first layer close to the surface is also studied on one hand, calculating Minkowski parameters and the Shannon entropy of the patterns of the 2D density maps of the anions placed there and, on the other hand, computing the 2D-Fourier transform of the positions of these anions. Our results are compared with those obtained previously for the same mixtures confined between two graphene walls. Although similarities exist between both cases, interesting differences are observed in the lateral structure that the ionic liquid adopts near borophene interfaces due to their strong anisotropy. In particular, we have observed that borophene induces more markedly ordered 2D patterns in the innermost layer of the ionic liquid electric double layer, specially when they are charged. It is this feature that makes borophene a potential candidate for battery electrode applications with possibilities beyond those of graphene.Ministerio de Economía, Industria y Competitividad ((Projects MAT2017-89239-C2-1-P, MAT2017-89239-C2-2-P, CTQ2015-65816-R and PGC2018-093745-B-I00)Xunta de Galicia (ED431D 2017/06, ED431E 2018/08 and GRC ED431C 2016/001)Junta de Castilla y León (Ref. project VA124G18

Search for Scalar Diphoton Resonances in the Mass Range 65−60065-600 GeV with the ATLAS Detector in pppp Collision Data at s\sqrt{s} = 8 TeVTeV

A search for scalar particles decaying via narrow resonances into two photons in the mass range 65–600 GeV is performed using $20.3\text{}\text{}{\mathrm{fb}}^{-1}$ of $\sqrt{s}=8\text{}\text{}\mathrm{TeV}$ $pp$ collision data collected with the ATLAS detector at the Large Hadron Collider. The recently discovered Higgs boson is treated as a background. No significant evidence for an additional signal is observed. The results are presented as limits at the 95% confidence level on the production cross section of a scalar boson times branching ratio into two photons, in a fiducial volume where the reconstruction efficiency is approximately independent of the event topology. The upper limits set extend over a considerably wider mass range than previous searches

Search for Higgs and ZZ Boson Decays to J/ψγJ/\psi\gamma and Υ(nS)γ\Upsilon(nS)\gamma with the ATLAS Detector

A search for the decays of the Higgs and $Z$ bosons to $J/\psi\gamma$ and $\Upsilon(nS)\gamma$ ($n=1,2,3$) is performed with $pp$ collision data samples corresponding to integrated luminosities of up to $20.3\mathrm{fb}^{-1}$ collected at $\sqrt{s}=8\mathrm{TeV}$ with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above expected backgrounds and 95% CL upper limits are placed on the branching fractions. In the $J/\psi\gamma$ final state the limits are $1.5\times10^{-3}$ and $2.6\times10^{-6}$ for the Higgs and $Z$ bosons, respectively, while in the $\Upsilon(1S,2S,3S)\,\gamma$ final states the limits are $(1.3,1.9,1.3)\times10^{-3}$ and $(3.4,6.5,5.4)\times10^{-6}$, respectively

Finska tingsdomares bedömningar av partsutlåtanden givna på plats i rätten eller via videokonferens

Professionals within the judicial system sometimes believe they can assess whether someone is lying or not based on cues such as body language and emotional expression. Research has, however, shown that this is impossible. The Finnish Supreme Court has also given rulings in accordance with this demonstrated fact. There has also been previous research on whether party or witness statements are assessed differently in court depending on whether they are given live, via videoconference, or via prerecorded video. In the present study, we investigated how a Finnish sample of district judges (N=47) assigned probative value to different variables concerning the statement or the statement giver, such as body language and emotional expression. We also investigated the connection between the judges’ beliefs about the relevance of body language and emotional expression and their preference for live statements or statements via videoconference. The judges reported assigning equal amounts of probative value to statements given live and statements given via videoconference. However, judges found it easier to detect deception live, and this preference correlated with how relevant they thought body language is when assessing the probative value of the statement. In other words, a slight bias to assess live statements more favorably than statements given via videoconference might still exist. More effort needs to be put into making judges and Supreme Courts aware of robust scientific results that have been the subject of decades of research, such as the fact that one cannot assess whether someone is lying or not based on cues such as body language

Search for Scalar-Charm pair production in pp collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

The results of a dedicated search for pair production of scalar partners of charm quarks are reported. The search is based on an integrated luminosity of 20.3 fb$^{-1}$ of pp collisions at $\sqrt{s}=8$ TeV recorded with the ATLAS detector at the LHC. The search is performed using events with large missing transverse momentum and at least two jets, where the two leading jets are each tagged as originating from c-quarks. Events containing isolated electrons or muons are vetoed. In an R-parity-conserving minimal supersymmetric scenario in which a single scalar-charm state is kinematically accessible, and where it decays exclusively into a charm quark and a neutralino, 95% confidence-level upper limits are obtained in the scalar-charm-neutralino mass plane such that, for neutralino masses below 200 GeV, scalar-charm masses up to 490 GeV are excluded

Search for Higgs and Z Boson Decays to J/ψγJ/\psi\gamma and Υ(nS)γ\Upsilon(nS)\gamma with the ATLAS Detector

A search for the decays of the Higgs and Z bosons to J/ψγ and ϒ(nS)γ (n=1,2,3) is performed with pp collision data samples corresponding to integrated luminosities of up to 20.3 fb-1 collected at s=8 TeV with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above expected backgrounds and 95% C.L. upper limits are placed on the branching fractions. In the J/ψγ final state the limits are 1.5×10-3 and 2.6×10-6 for the Higgs and Z boson decays, respectively, while in the ϒ(1S,2S,3S)γ final states the limits are (1.3,1.9,1.3)×10-3 and (3.4,6.5,5.4)×10-6, respectively

Measurement of differential J/ψJ/\psi production cross-sections and forward-backward ratio in p+Pb collisions with the ATLAS detector

Measurements of differential cross-sections for $J/\psi$ production in p+Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV at the LHC with the ATLAS detector are presented. The data set used corresponds to an integrated luminosity of 28.1 nb$^{-1}$. The $J/\psi$ mesons are reconstructed in the dimuon decay channel over the transverse momentum range $8<p_{\mathrm{T}}<30$ GeV and over the center-of-mass rapidity range $-2.87<y^{*}<1.94$. Prompt $J/\psi$ are separated from $J/\psi$ resulting from $b$-hadron decays through an analysis of the distance between the $J/\psi$ decay vertex and the event primary vertex. The differential cross-section for production of nonprompt $J/\psi$ is compared to a FONLL calculation that does not include nuclear effects. Forward-backward production ratios are presented and compared to theoretical predictions. These results constrain the kinematic dependence of nuclear modifications of charmonium and $b$-quark production in p+Pb collisions