Searching for Z′ bosons at the P2 experiment

The P2 experiment aims at high-precision measurements of the parity-violating asymmetry in elastic electron-proton and electron-12C scatterings with longitudinally polarized electrons. We discuss here the sensitivity of P2 to new physics mediated by an additional neutral gauge boson Z′ of a new U(1)′ gauge symmetry. If the charge assignment of the U(1)′ is chiral, i.e., left- and right-handed fermions have different charges under U(1)′, additional parity-violation is induced directly. On the other hand, if the U(1)′ has a non-chiral charge assignment, additional parity-violation can be induced via mass or kinetic Z-Z′ mixing. By comparing the P2 sensitivity to existing constraints, we show that in both cases P2 has discovery potential over a wide range of Z′ mass. In particular, for chiral models, the P2 experiment can probe gauge couplings at the order of 10−5 when the Z′ boson is light, and heavy Z′ bosons up to 79 (90) TeV in the proton (12C) mode. For non-chiral models with mass mixing, the P2 experiment is sensitive to mass mixing angles smaller than roughly 10−4, depending on model details and gauge coupling magnitude.

Explaining Atomki anomaly and muon g − 2 in U(1)X extended flavour violating two Higgs doublet model

We investigate a two Higgs doublet model with extra flavour depending U(1)X gauge symmetry where Z′ boson interactions can explain the Atomki anomaly by choosing appropriate charge assignment for the SM fermions. For parameter region explaining the Atomki anomaly we obtain light scalar boson with $$ \mathcal{O} $$ O (10) GeV mass, and we explore scalar sector to search for allowed parameter space. We then discuss anomalous magnetic dipole moment of muon and lepton flavour violating processes induced by Yukawa couplings of our model.

A note on gauge anomaly cancellation in effective field theories

The conditions for the absence of gauge anomalies in effective field theories (EFT) are rivisited. General results from the cohomology of the BRST operator do not prevent potential anomalies arising from the non-renormalizable sector, when the gauge group is not semi-simple, like in the Standard Model EFT (SMEFT). By considering a simple explicit model that mimics the SMEFT properties, we compute the anomaly in the regularized theory, including a complete set of dimension six operators. We show that the dependence of the anomaly on the non-renormalizable part can be removed by adding a local counterterm to the theory. As a result the condition for gauge anomaly cancellation is completely controlled by the charge assignment of the fermion sector, as in the renormalizable theory.

A counterexample to the Nelson-Seiberg theorem

We present a counterexample to the Nelson-Seiberg theorem and its extensions. The model has 4 chiral fields, including one R-charge 2 field and no R-charge 0 filed. Giving generic values of coefficients in the renormalizable superpotential, there is a supersymmetric vacuum with one complex dimensional degeneracy. The superpotential equals zero and the R-symmetry is broken everywhere on the degenerated vacuum. The existence of such a vacuum disagrees with both the original Nelson-Seiberg theorem and its extensions, and can be viewed as the consequence of a non-generic R-charge assignment. Such counterexamples may introduce error to the field counting method for surveying the string landscape, and are worth further investigations.

Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning

Motivation Partial atomic charges are usually used to calculate the electrostatic component of energy in many molecular modeling applications, such as molecular docking, molecular dynamics simulations, free energy calculations and so forth. High-level quantum mechanics calculations may provide the most accurate way to estimate the partial charges for small molecules, but they are too time-consuming to be used to process a large number of molecules for high throughput virtual screening. Results We proposed a new molecule descriptor named Atom-Path-Descriptor (APD) and developed a set of APD-based machine learning (ML) models to predict the partial charges for small molecules with high accuracy. In the APD algorithm, the 3D structures of molecules were assigned with atom centers and atom-pair path-based atom layers to characterize the local chemical environments of atoms. Then, based on the APDs, two representative ensemble ML algorithms, i.e. random forest (RF) and extreme gradient boosting (XGBoost), were employed to develop the regression models for partial charge assignment. The results illustrate that the RF models based on APDs give better predictions for all the atom types than those based on traditional molecular fingerprints reported in the previous study. More encouragingly, the models trained by XGBoost can improve the predictions of partial charges further, and they can achieve the average root-mean-square error 0.0116 e on the external test set, which is much lower than that (0.0195 e) reported in the previous study, suggesting that the proposed algorithm is quite promising to be used in partial charge assignment with high accuracy. Availability and implementation The software framework described in this paper is freely available at https://github.com/jkwang93/Atom-Path-Descriptor-based-machine-learning Supplementary information Supplementary data are available at Bioinformatics online.

Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans

Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical (QC) calculations are critical for determining the conformational distributions of small molecules, but are computationally expensive and scale poorly with molecular size. To reduce computational cost and avoid the complications of distal through-space intramolecular interactions, molecules are generally fragmented into smaller entities to carry out QC torsion scans. However, torsion potentials, particularly for conjugated bonds, can be strongly affected by through-bond chemistry distal to the torsion itself. Poor fragmentation schemes have the potential to significantly disrupt electronic properties in the region around the torsion by removing important, distal chemistries, leading to poor representation of the parent molecule’s chemical environment and the resulting torsion energy profile. Here we show that a rapidly computable quantity, the fractional Wiberg bond order (WBO), is a sensitive reporter on whether the chemical environment around a torsion has been disrupted. We show that the WBO can be used as a surrogate to assess the robustness of fragmentation schemes and identify conjugated bond sets. We use this concept to construct a validation set by exhaustively fragmenting a set of druglike organic molecules and examine their corresponding WBO distributions derived from accessible conformations that can be used to evaluate fragmentation schemes. To illustrate the utility of the WBO in assessing fragmentation schemes that preserve the chemical environment, we propose a new fragmentation scheme that uses rapidly-computable AM1 WBOs, which are available essentially for free as part of standard AM1-BCC partial charge assignment. This approach can simultaneously maximize the chemical equivalency of the fragment and the substructure in the larger molecule while minimizing fragment size to accelerate QC torsion potential computation for small molecules and reducing undesired through-space steric interactions.

Role of partial charge assignment methods in high-throughput screening of MOF adsorbents and membranes for CO2/CH4 separation

The role of partial charge assignment methods used in high-throughput computational screening of metal organic frameworks (MOFs) for CO2/CH4 separation is examined.