Toward detection of electron-hole pair excitation in H-atom collisions with Au(111): Adiabatic molecular dynamics with a semi-empirical full-dimensional potential energy surface.

We report an analytic potential energy surface (PES) based on several hundred DFT energies for H interacting with a Au(111) surface. Effective medium theory is used to fit the DFT data, which were obtained for the Au atoms held at their equilibrium positions. This procedure also provides an adequate treatment of the PES for displacements of Au atoms that occur during scattering of H atoms. The fitted PES is compared to DFT energies obtained from ab initio molecular dynamics trajectories. We present molecular dynamics simulations of energy and angle resolved scattering probabilities at five incidence angles at an incidence energy, Ei = 5 eV, and at a surface temperature, TS = 10 K. Simple single bounce trajectories are important at all incidence conditions explored here. Double bounce events also make up a significant fraction of the scattering. A qualitative analysis of the double-bounce events reveals that most occur as collisions of an H-atom with two neighboring surface gold atoms. The energy losses observed are consistent with a simple binary collision model, transferring typically less than 150 meV to the solid per bounce

Imposing Correct Jellium Response Is Key to Predict the Density Response by Orbital-Free DFT

Orbital-free density functional theory (OF-DFT) constitutes a computationally highly effective tool for modeling electronic structures of systems ranging from room-temperature materials to warm dense matter. Its accuracy critically depends on the employed kinetic energy (KE) density functional, which has to be supplied as an external input. In this work we consider several nonlocal and Laplacian-level KE functionals and use an external harmonic perturbation to compute the static density response at T=0 K in the linear and beyond linear response regimes. We test for the satisfaction of exact conditions in the limit of uniform densities and for how approximate KE functionals reproduce the density response of realistic materials (e.g., Al and Si) against the Kohn-Sham DFT reference which employs the exact KE. The results illustrate that several functionals violate exact conditions in the UEG limit. We find a strong correlation between the accuracy of the KE functionals in the UEG limit and in the strongly inhomogeneous case. This empirically demonstrates the importance of imposing the limit of UEG response for uniform densities and validates the use of the Lindhard function in the formulation of kernels for nonlocal functionals. This conclusion is substantiated by additional calculations for bulk Aluminum (Al) with a face-centered cubic (fcc) lattice and Silicon (Si) with an fcc lattice, body-centered cubic (bcc) lattice, and semiconducting crystal diamond (cd) state. The analysis of fcc Al, and fcc as well as bcc Si data follows closely the conclusions drawn for the UEG, allowing us to extend our conclusions to realistic systems that are subject to density inhomogeneities induced by ions

eQE: An open‐source density functional embedding theory code for the condensed phase

AbstractIn this work, we present the main features and algorithmic details of a novel implementation of the frozen density embedding (FDE) formulation of subsystem density functional theory (DFT) that is specifically designed to enable ab initio molecular dynamics (AIMD) simulations of large‐scale condensed‐phase systems containing 1000s of atoms. This code (available at http://eqe.rutgers.edu) has been given the moniker of embedded Quantum ESPRESSO (eQE) as it is a generalization of the open‐source Quantum ESPRESSO (QE) suite of programs. The strengths of eQE reside in a hierarchical parallelization scheme that allows for an efficient and fully self‐consistent treatment of the electronic structure (via the addition of an additional DIIS extrapolation layer) while simultaneously exploiting the inherent symmetries and periodicities in the system (via sampling of subsystem‐specific first Brillouin zones and utilization of subsystem‐specific basis sets). While bulk liquids and molecular crystals are two classes of systems that exemplify the utility of the FDE approach (as these systems can be partitioned into weakly interacting subunits), we show that eQE has significantly extended this regime of applicability by outperforming standard semilocal Kohn–Sham DFT (KS‐DFT) for large‐scale heterogeneous catalysts with quite different layer‐specific electronic structure and intrinsic periodicities. eQE features very favorable strong parallel scaling for a model system of bulk liquid water composed of 256 water molecules, which allows for a significant decrease in the overall time to solution when compared to KS‐DFT. We show that eQE achieves speedups greater than one order of magnitude ( ) when performing AIMD simulations of such large‐scale condensed‐phase systems as: (1) molecular liquids via bulk liquid water represented by 1024 independent water molecules (3072 atoms with a 25.3× speedup over KS‐DFT), (2) polypeptide/biomolecule solvation via (gly)6 solvated in (H2O)395 (1230 atoms with a 38.6× speedup over KS‐DFT), and (3) molecular crystals via a 3 × 3 × 3 periodic supercell of pentacene (1940 atoms with a 12.0× speedup over KS‐DFT). These results represent a significant improvement over the current state‐of‐the‐art and now enable subsystem DFT‐based AIMD simulations of realistically sized condensed‐phase systems of interest throughout chemistry, physics, and materials science

Solvation effects on halides core spectra with Multilevel Real-Time quantum embedding

In this work we introduce a novel subsystem-based electronic structure embedding method that combines the projection-based block-orthogonalized Manby-Miller embedding (BOMME) with the density-based Frozen Density Embedding (FDE) methods. Our approach is effective for systems in which the building blocks interact at varying strengths while still maintaining a lower computational cost compared to a quantum simulation of the entire system. To evaluate the performance of our method, we assess its ability to reproduce the X-ray absorption spectra (XAS) of chloride and fluoride anions in aqueous solutions (based on a 50-water droplet model) via real-time time-dependent density functional theory (rt-TDDFT) calculations. We employ an ensemble approach to compute XAS for the K- and L-edges, utilizing multiple snapshots of configuration space obtained from classical molecular dynamics simulations with a polarizable force field. Configurational averaging influences both the broadening of spectral features and their intensities, with contributions to the final intensities originating from different geometry configurations. We found that embedding models that are too approximate for halide-water specific interactions, as in the case of FDE, fail to reproduce the experimental spectrum for chloride. Meanwhile, BOMME tends to overestimate intensities, particularly for higher energy features because of finite-size effects. Combining FDE for the second solvation shell and retaining BOMME for the first solvation shell mitigates this effect, resulting in an overall improved agreement within the energy range of the experimental spectrum. Additionally, we compute the transition densities of the relevant transitions, confirming that these transitions occur within the halide systems. Thus, our real-time QM/QM/QM embedding method proves to be a promising approach for modeling XAS of solvated systems

Treatment with fibrates is associated with higher LAL activity in dyslipidemic patients

Lysosomal acid lipase (LAL) is responsible for the hydrolysis of cholesteryl esters (CE) and triglycerides (TG) within the lysosomes; generated cholesterol and free fatty acids (FFA) are released in the cytosol where they can regulate their own synthesis and metabolism. When LAL is not active, as in case of genetic mutations, CE and TG accumulate in the lysosomal compartment, while the lack of release of cholesterol and FFA in the cytosol leads to an upregulation of their synthesis. Thus, LAL plays a central role in the intracellular homeostasis of lipids. Since there are no indications about the effect of different lipid-lowering agents on LAL activity, aim of the study was to address the relationship between LAL activity and the type of lipid-lowering therapy in a cohort of dyslipidemic patients. LAL activity was measured on dried blood spot from 120 patients with hypercholesterolemia or mixed dyslipidemia and was negatively correlated to LDL-cholesterol levels. Among enrolled patients, ninety-one were taking one or more lipid-lowering drugs, as statins, fibrates, ezetimibe and omega-3 polyunsaturated fatty acids. When patients were stratified according to the type of lipid-lowering treatment, i.e. untreated, taking statins or taking fibrates, LAL activity was significantly higher in those with fibrates, even after adjustment for sex, age, BMI, lipid parameters, liver function, metabolic syndrome, diabetes and statin use. In a subset of patients tested after 3 months of treatment with micronized fenofibrate, LAL activity raised by 21%; the increase was negatively correlated with baseline LAL activity. Thus, the use of fibrates is independently associated with higher LAL activity in dyslipidemic patients, suggesting that the positive effects of PPAR-\u3b1 activation on cellular and systemic lipid homeostasis can also include an improved LAL activity

Charge-based continuous model for long-channel Symmetric Double-Gate Junctionless Transistors

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Noninvasive Assessment of Hemodynamic Stress Distribution after Indirect Revascularization for Pediatric Moyamoya Vasculopathy

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Rare Germline Genetic Variants and the Risks of Epithelial Ovarian Cancer.

A family history of ovarian or breast cancer is the strongest risk factor for epithelial ovarian cancer (EOC). Germline deleterious variants in the BRCA1 and BRCA2 genes confer EOC risks by age 80, of 44% and 17% respectively. The mismatch repair genes, particularly MSH2 and MSH6, are also EOC susceptibility genes. Several other DNA repair genes, BRIP1, RAD51C, RAD51D, and PALB2, have been identified as moderate risk EOC genes. EOC has five main histotypes; high-grade serous (HGS), low-grade serous (LGS), clear cell (CCC), endometrioid (END), and mucinous (MUC). This review examines the current understanding of the contribution of rare genetic variants to EOC, focussing on providing frequency data for each histotype. We provide an overview of frequency and risk for pathogenic variants in the known susceptibility genes as well as other proposed genes. We also describe the progress to-date to understand the role of missense variants and the different breast and ovarian cancer risks for each gene. Identification of susceptibility genes have clinical impact by reducing disease-associated mortality through improving risk prediction, with the possibility of prevention strategies, and developing new targeted treatments and these clinical implications are also discussed