Introducing “Identification Probability” for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies
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Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner–Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. Lastly, by modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.
A DP4 protocol has been successfully utilized to establish the true structure of the natural product cyclocinamide A, a flexible cyclic peptide with four isolated stereocenters. Benchmarking the necessary level of theory required to successfully predict the NMR spectra of three previously synthesized isomers of cyclocinamide A led to the prediction of the natural stereochemistry as 4 S, 7 R, 11 R, 14 S, which has been confirmed by total synthesis.
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Abstract We thank the Comment's authors for their considered critique of our paper. We respond to their main criticisms and hope that this discussion motivates further consideration of communication strategies for event attribution analyses.
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The first theoretical exploration of superhalogen properties of polynuclear structures based on pseudohalogen ligand is reported here via a case study on eight triply-bridged [Mg{sub 2}(CN){sub 5}]{sup −} clusters. From our high-level ab initio results, all these clusters are superhalogens due to their high vertical electron detachment energies (VDE), of which the largest value is 8.67 eV at coupled-cluster single double triple (CCSD(T)) level. Although outer valence Green's function results are consistent with CCSD(T) in most cases, it overestimates the VDEs of three anions dramatically by more than 1 eV. Therefore, the combined usage of several theoretical methods is important for the accuracy of purely theoretical prediction of superhalogen properties of new structures. Spatial distribution of the extra electron of high-VDE anions here indicates two features: remarkable aggregation on bridging CN units and non-negligible distribution on every CN unit. These two features lower the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to detachment of CN{sup −1} were also investigated for these anions. The collection of these results indicates that polynuclear structures based on pseudohalogen ligand are promising candidates for new superhalogens with enhanced properties.
Current Monte Carlo codes use one of three models: (1) the asymptotic scattering model, (2) the free gas scattering model, or (3) the S(α,β) model, depending on the neutron energy and the specific Monte Carlo code. This thesis addresses the consequences of using the free gas scattering model, which assumes that the neutron interacts with atoms in thermal motion in a monatomic gas in thermal equilibrium at material temperature, T. Most importantly, the free gas model assumes the scattering cross section is constant over the neutron energy range, which is usually a good approximation for light nuclei, but not for heavy nuclei where the scattering cross section may have several resonances in the epithermal region. Several researchers in the field have shown that the exact resonance scattering model is temperaturedependent, and neglecting the resonances in the lower epithermal range can under-predict resonance absorption due to the upscattering phenomenon mentioned above, leading to an over-prediction of keff by several hundred pcm. Existing methods to address this issue involve changing the neutron weights or implementing an extra rejection scheme in the free gas sampling scheme, and these all involve performing the collision analysis in the center-of-mass frame, followed by a conversion back to the laboratory frame to continue the random walk of the neutron. The goal of this paper was to develop a sampling methodology that (1) accounted for the energydependent scattering cross sections in the collision analysis and (2) was performed in the laboratory frame,avoiding the conversion to the center-of-mass frame. The energy dependence of the scattering cross section was modeled with even-ordered polynomials (2nd and 4th order) to approximate the scattering cross section in Blackshaw’s equations for the moments of the differential scattering PDFs. These moments were used to sample the outgoing neutron speed and angle in the laboratory frame on-the-fly during the random walk of the neutron. Results for criticality studies on fuel pin and fuel assembly calculations using methods developed in this dissertation showed very close comparison to results using the reference Dopplerbroadened rejection correction (DBRC) scheme.
Big Area Additive Manufacturing (BAAM) of composites requires significant time, energy, and material, so it is critical to reduce production inefficiencies to make functional parts without multiple iterations. Statistical process control coupled with Principal Component Analysis (PCA) is a powerful technique that provides a quick, computationally inexpensive, and intuitive way for operators to detect defects that form in a manufacturing process without massive datasets. Recently, a combined index that is a weighted sum of the Hotelling's T 2 and squared residual error statistics has been proposed that can be monitored in one chart, improving interpretation accuracy and simplicity. However, the literature does not offer a formal method to optimise the weights. Here, we introduce two new approaches to the traditional weight selection approach using simulated and BAAM image data. Approach 1 uses a theoretically motivated optimum inspired by probabilistic principal component analysis. Approach 2 systematically varies the ratio of the weights to find the optimum. We show that approach 1 delivers optimal anomaly detection performance in select cases while approach 2 fares better in practice. Surprisingly, we also show that choosing a more complex PCA model has a minimal negative impact on anomaly detection performance compared to a more simplistic model.
From 2001-2008, we use full-disk, SOHO/EIT 195 A calibrated images to determine latitudinal and day-to-day variations of the rotation rates of coronal holes (CHs). We estimate the weighted average of heliographic coordinates such as latitude and longitude from the central meridian on the observed solar disk. For different latitude zones between 40 Degree-Sign north and 40 Degree-Sign south, we compute rotation rates and find that, irrespective of their area, the number of days observed on the solar disk, and their latitudes, CHs rotate rigidly. Combined for all the latitude zones, we also find that CHs rotate rigidly during their evolution history. In addition, for all latitude zones, CHs follow a rigid body rotation law during their first appearance. Interestingly, the average first rotation rate ({approx}438 nHz) of CHs, computed from their first appearance on the solar disk, matches the rotation rate of the solar interior only below the tachocline.