Using first principles calculations we investigate the binding and diffusion of Li on silicene and evaluate the prospects for application to Li-ion batteries. We find that the defect formation energy for silicene is half that of graphene, showing that silicene is more likely to contain defects. The overall lithium adsorption energy on silicene with defects is greater than the bulk cohesive energy of lithium giving stability for use in storage. Our results predict high mobility for lithium atoms on the surface of silicene with energy barriers in the range of 0.28-0.30 eV. Further, we find that the diffusion barrier through silicene is significantly lower than the diffusion barrier through graphene, with a value of 0.05 eV for the double vacancy and 0.88 eV for the single vacancy. The low diffusion barriers, both on the surface and through the hollow site, suggest a suitable material for use in Li-ion batteries.

The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host–guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host–guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach (ATM/GAFF2-AM1BCC/TIP3P/HREM) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons; for example, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group sampling and/or guest starting pose, providing guidance to help improve future studies on these systems.

A significant challenge to making targeted cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies accessible to all individuals with cystic fibrosis (CF) are many mutations in the CFTR gene that can cause CF, most of which remain uncharacterized. Here, we characterized the structural and functional defects of the rare CFTR mutation R352Q, with a potential role contributing to intrapore chloride ion permeation, in patient-derived cell models of the airway and gut. CFTR function in differentiated nasal epithelial cultures and matched intestinal organoids was assessed using an ion transport assay and forskolin-induced swelling assay, respectively. CFTR potentiators (VX-770, GLPG1837, and VX-445) and correctors (VX-809, VX-445, with or without VX-661) were tested. Data from R352Q-CFTR were compared with data of 20 participants with mutations with known impact on CFTR function. R352Q-CFTR has residual CFTR function that was restored to functional CFTR activity by CFTR potentiators but not the corrector. Molecular dynamics simulations of R352Q-CFTR were carried out, which indicated the presence of a chloride conductance defect, with little evidence supporting a gating defect. The combination approach of in vitro patient-derived cell models and in silico molecular dynamics simulations to characterize rare CFTR mutations can improve the specificity and sensitivity of modulator response predictions and aid in their translational use for CF precision medicine.

The damping of plasmons due to structural disorder may have important practical consequences. Here we use spherical harmonic expansions to quantify the damping of plasmons of ensembles of closely coupled sphere chains with moderately disordered gaps.We show that the quadratic shift of average resonance position due to disorder is maintained in the transition from weak to close coupling, but the sensitivity to disorder increases.Further we find that although the main peak is most often damped and broadened by disorder, it is possible for the optical extinction of disordered gold chains to increase slightly due to red-skew into a region with more favorable metal properties.