Transfer learning for affordable and high quality tunneling splittings from instanton calculations

The combination of transfer learning (TL) a low level potential energy surface (PES) to a higher level of electronic structure theory together with ring-polymer instanton (RPI) theory is explored and applied to malonaldehyde. The RPI approach provides a semiclassical approximation of the tunneling splitting and depends sensitively on the accuracy of the PES. With second order M{\o}ller-Plesset perturbation theory (MP2) as the low-level (LL) model and energies and forces from coupled cluster singles, doubles and perturbative triples (CCSD(T)) as the high-level (HL) model, it is demonstrated that CCSD(T) information from only 25 to 50 judiciously selected structures along and around the instanton path suffice to reach HL-accuracy for the tunneling splitting. In addition, the global quality of the HL-PES is demonstrated through a mean average error of 0.3 kcal/mol for energies up to 40 kcal/mol above the minimum energy structure (a factor of 2 higher than the energies employed during TL) and $< 2$ cm$^{-1}$ for harmonic frequencies compared with computationally challenging normal mode calculations at the CCSD(T) level

ML Models of Vibrating H2_2CO: Comparing Reproducing Kernels, FCHL and PhysNet

Machine Learning (ML) has become a promising tool for improving the quality of atomistic simulations. Using formaldehyde as a benchmark system for intramolecular interactions, a comparative assessment of ML models based on state-of-the-art variants of deep neural networks (NN), reproducing kernel Hilbert space (RKHS+F), and kernel ridge regression (KRR) is presented. Learning curves for energies and atomic forces indicate rapid convergence towards excellent predictions for B3LYP, MP2, and CCSD(T)-F12 reference results for modestly sized (in the hundreds) training sets. Typically, learning curve off-sets decay as one goes from NN (PhysNet) to RKHS+F to KRR (FCHL). Conversely, the predictive power for extrapolation of energies towards new geometries increases in the same order with RKHS+F and FCHL performing almost equally. For harmonic vibrational frequencies, the picture is less clear, with PhysNet and FCHL yielding respectively flat learning at $\sim$ 1 and $\sim$ 0.2 cm$^{-1}$ no matter which reference method, while RKHS+F models level off for B3LYP, and exhibit continued improvements for MP2 and CCSD(T)-F12. Finite-temperature molecular dynamics (MD) simulations with the same initial conditions yield indistinguishable infrared spectra with good performance compared with experiment except for the high-frequency modes involving hydrogen stretch motion which is a known limitation of MD for vibrational spectroscopy. For sufficiently large training set sizes all three models can detect insufficient convergence (``noise'') of the reference electronic structure calculations in that the learning curves level off. Transfer learning (TL) from B3LYP to CCSD(T)-F12 with PhysNet indicates that additional improvements in data efficiency can be achieved

Sero-Epidemiology as a Tool to Screen Populations for Exposure to Mycobacterium ulcerans

Sero-epidemiological analyses revealed that a higher proportion of sera from individuals living in the Buruli ulcer (BU) endemic Densu River Valley of Ghana contain Mycobacterium ulcerans 18 kDa small heat shock protein (shsp)-specific IgG than sera from inhabitants of the Volta Region, which was regarded so far as BU non-endemic. However, follow-up studies in the Volta Region showed that the individual with the highest anti-18 kDa shsp-specific serum IgG titer of all participants from the Volta Region had a BU lesion. Identification of more BU patients in the Volta Region by subsequent active case search demonstrated that sero-epidemiology can help identify low endemicity areas. Endemic and non-endemic communities along the Densu River Valley differed neither in sero-prevalence nor in positivity of environmental samples in PCR targeting M. ulcerans genomic and plasmid DNA sequences. A lower risk of developing M. ulcerans disease in the non-endemic communities may either be related to host factors or a lower virulence of local M. ulcerans strains

LPMLE3 : a novel 1-D approach to study water flow in streambeds using heat as a tracer

We introduce LPMLE3, a new 1-D approach to quantify vertical water flow components at streambeds using temperature data collected in different depths. LPMLE3 solves the partial differential equation for coupled water flow and heat transport in the frequency domain. Unlike other 1-D approaches it does not assume a semi-infinite halfspace with the location of the lower boundary condition approaching infinity. Instead, it uses local upper and lower boundary conditions. As such, the streambed can be divided into finite subdomains bound at the top and bottom by a temperature-time series. Information from a third temperature sensor within each subdomain is then used for parameter estimation. LPMLE3 applies a low order local polynomial to separate periodic and transient parts (including the noise contributions) of a temperature-time series and calculates the frequency response of each subdomain to a known temperature input at the streambed top. A maximum-likelihood estimator is used to estimate the vertical component of water flow, thermal diffusivity, and their uncertainties for each streambed subdomain and provides information regarding model quality. We tested the method on synthetic temperature data generated with the numerical model STRIVE and demonstrate how the vertical flow component can be quantified for field data collected in a Belgian stream. We show that by using the results in additional analyses, nonvertical flow components could be identified and by making certain assumptions they could be quantified for each subdomain. LPMLE3 performed well on both simulated and field data and can be considered a valuable addition to the existing 1-D methods

The polarization observables T, P, and H and their impact on γp→pπ0\gamma p \to p\pi^0 multipoles

Data on the polarization observables T, P, and H for the reaction $\gamma p\to p\pi^0$ are reported. Compared to earlier data from other experiments, our data are more precise and extend the covered range in energy and angle substantially. The results were extracted from azimuthal asymmetries measured using a transversely polarized target and linearly polarized photons. The data were taken at the Bonn electron stretcher accelerator ELSA with the CBELSA/TAPS detector. Within the Bonn-Gatchina partial wave analysis, the new polarization data lead to a significant narrowing of the error band for the multipoles for neutral-pion photoproduction

Photoproduction of π0\pi^0-pairs off protons and off neutrons

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of $\pi^0\pi^0$ pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557~MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400~MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. The results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15\%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final state invariant masses up to $\approx$1550~MeV), where both reactions are dominated by the $N(1520)3/2^-\rightarrow \Delta(1232)3/2^+\pi$ decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an $N^{\star}\rightarrow N\sigma$ decay for the proton, while the reaction is dominated by a sequential decay via a $\Delta\pi$ intermediate state for the neutron. The data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled channel analysis.Comment: accepted for publication in Eur. Phys. J.

The N(1520) 3/2- helicity amplitudes from an energy-independent multipole analysis based on new polarization data on photoproduction of neutral pions

New data on the polarization observables T, P, and H for the reaction $\gamma p \to p\pi^0$ are reported. The results are extracted from azimuthal asymmetries when a transversely polarized butanol target and a linearly polarized photon beam are used. The data were taken at the Bonn electron stretcher accelerator ELSA using the CBELSA/TAPS detector. These and earlier data are used to perform a truncated energy-independent partial wave analysis in sliced-energy bins. This energy-independent analysis is compared to the results from energy-dependent partial wave analyses

Photoproduction of π0-pairs off protons and off neutrons

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of π0π0 pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. The results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final-state invariant masses up to ≈1550 MeV), where both reactions are dominated by the N(1520)3/2−→Δ(1232)3/2+π decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an N⋆→Nσ decay for the proton, while the reaction is dominated by a sequential decay via a Δπ intermediate state for the neutron. The data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled-channel analysis

Quasifree photoproduction of η\eta mesons off protons and neutrons

Differential and total cross sections for the quasifree reactions $\gamma p\rightarrow\eta p$ and $\gamma n\rightarrow\eta n$ have been determined at the MAMI-C electron accelerator using a liquid deuterium target. Photons were produced via bremsstrahlung from the 1.5 GeV incident electron beam and energy-tagged with the Glasgow photon tagger. Decay photons of the neutral decay modes $\eta\rightarrow 2\gamma$ and $\eta\rightarrow 3\pi^0 \rightarrow 6\gamma$ and coincident recoil nucleons were detected in a combined setup of the Crystal Ball and the TAPS calorimeters. The $\eta$-production cross sections were measured in coincidence with recoil protons, recoil neutrons, and in an inclusive mode without a condition on recoil nucleons, which allowed a check of the internal consistency of the data. The effects from nuclear Fermi motion were removed by a kinematic reconstruction of the final-state invariant mass and possible nuclear effects on the quasifree cross section were investigated by a comparison of free and quasifree proton data. The results, which represent a significant improvement in statistical quality compared to previous measurements, agree with the known neutron-to-proton cross-section ratio in the peak of the $S_{11}(1535)$ resonance and confirm a peak in the neutron cross section, which is absent for the proton, at a center-of-mass energy $W = (1670\pm 5)$ MeV with an intrinsic width of $\Gamma\approx 30$ MeV

The isospin structure of photoproduction of pi-eta pairs from the nucleon in the threshold region

Photoproduction of $\pi\eta$-pairs from nucleons has been investigated from threshold up to incident photon energies of $\approx$~1.4~GeV. The quasi-free reactions $\gamma p\rightarrow p\pi^0\eta$, $\gamma n\rightarrow n\pi^0\eta$, $\gamma p\rightarrow n\pi^+\eta$, and $\gamma n\rightarrow p\pi^-\eta$ were for the first time measured from nucleons bound in the deuteron. The corresponding reactions from a free-proton target were also studied to investigate final-state interaction effects (for neutral pions the free-proton results could be compared to previous measurements; the $\gamma p\rightarrow n\pi^+\eta$ reaction was measured for the first time). For the $\pi^0\eta$ final state coherent production via the $\gamma d\rightarrow d\pi^0\eta$ reaction was also investigated. The experiments were performed at the tagged photon beam of the Mainz MAMI accelerator using an almost $4\pi$ coverage electromagnetic calorimeter composed of the Crystal Ball and TAPS detectors. The total cross sections for the four different final states obey the relation $\sigma(p\pi^0\eta)$ $\approx$ $\sigma(n\pi^0\eta)$ $\approx$ $2\sigma(p\pi^-\eta)$ $\approx$ $2\sigma(n\pi^+\eta)$ as expected for a dominant contribution from a $\Delta^{\star}\rightarrow\eta\Delta(1232)\rightarrow\pi\eta N$ reaction chain, which is also supported by the shapes of the invariant-mass distributions of nucleon-meson and $\pi$-$\eta$ pairs. The experimental results are compared to the predictions from an isobar reaction model.Comment: accepted for publication in Phys. Lett.