Comparison study of exchange-correlation functionals on prediction of ground states and structural properties

Despite significant advances in first-principles calculation methods, there is no single exchange-correlation functional which predicts the ground state of materials without an error yet. We investigated how accurately ground states of binary semiconductors are described using 16 exchange-correlation functionals (with or without van der Waals corrections). LDA, PBEsol, SCAN (with or without rVV10 correction), and PBE with D3 van der Waals correction (zero or Becke-Johnson damping) show good predicting power. The lattice constants of stable phases were slightly better described by SCAN, PBEsol, PBE+D3 (Becke-Johnson damping), and MS2. We also propose a set of functionals to double-check the stability of new materials based on the majority vote.     

从知识传授到育人:高职“生活中的化学”教学实践*

深挖高职院校公选课“生活中的化学”的育人元素,精心设计教学内容,运用课堂主题辩论、趣味生活实验的设计与展示、探秘生活中的化学等理论知识传授与课内外实践相结合的教学方式,实现全过程育人,充分展现了公选课在立德树人方面的价值。     

Regularity of optimal sets for some functional involving eigenvalues of an operator in divergence form

In this paper we consider minimizers of the functional$\min \{{\lambda }_1(\mathrm{\Omega })+\cdots +{\lambda }_k(\mathrm{\Omega })+\mathrm{\Lambda }|\mathrm{\Omega }|,:\mathrm{\Omega }\subset D\text{ open}\}$ where $D\subset {\mathbb{R}}^d$ is a bounded open set and where $0<{\lambda }_1(\mathrm{\Omega })\le \cdots \le {\lambda }_k(\mathrm{\Omega })$ are the first k eigenvalues on Ω of an operator in divergence form with Dirichlet boundary condition and with Hölder continuous coefficients. We prove that the optimal sets ${\mathrm{\Omega }}^{⁎}$ have finite perimeter and that their free boundary $\partial {\mathrm{\Omega }}^{⁎}\cap D$ is composed of a regular part, which is locally the graph of a $C^{1,\alpha }$-regular function, and a singular part, which is empty if $d<d^{⁎}$, discrete if $d=d^{⁎}$ and of Hausdorff dimension at most $d-d^{⁎}$ if $d>d^{⁎}$, for some $d^{⁎}\in \{5,6,7\}$.     

基于GA_XGBoost模型的大学生科研能力预测问题研究

科学评价大学生科研创新能力对我国科研水平的提高具有重要意义.采用机器学习模型来预测大学生科研能力可以起到良好的效果,提出一种GAXGBoost模型来实现对大学生的科研能力预测.此模型是以Xgboost算法为基础,然后充分利用遗传算法的全局搜索能力自动搜索Xgboost最优超参数,避免了人为经验调参不准确的缺陷,最后采用精英选择策略以此确保每一轮都是最佳的进化结果.通过分析表明,所采用的GAXGBoost模型在大学生科研能力预测的结果中具有很高的精度,将此模型与Logistic Regression、Random Forest、SVM等模型进行对比,GAXGBoost模型的预测精度最高.     

A Far-Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging

Far-red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far-red Fluorescence Activating and absorption Shifting Tag), a 14-kDa monomeric protein that forms a bright far-red fluorescent assembly with (4-hydroxy-3-methoxy-phenyl)allylidene rhodanine (HPAR-3OM). As HPAR-3OM is essentially non-fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR-3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae, and chicken embryos. Beyond enabling the genetic encoding of far-red fluorescence, frFAST allowed the design of a far-red chemogenetic reporter of protein–protein interactions, demonstrating its great potential for the design of innovative far-red emitting biosensors.     

Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling

The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter _γ-aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear ¹H and ¹³C nuclear magnetic resonance (NMR) experiments supported by density functional theory molecular modeling. The structures of three forms of free muscimol molecule both in the gas phase and in the presence of water solvent, modeled by polarized continuous model, and nuclear magnetic isotropic shieldings, the corresponding chemical shifts, and indirect spin–spin coupling constants were calculated. Several J-couplings observed in proton and carbon NMR spectra, not available before, are reported. The obtained experimental spectra, supported by theoretical calculations, favor the zwitterion form of muscimol in water. This structure differs from NH isomer, previously determined in dimethyl sulfoxide (DMSO) solution. In addition, positions of signals C3 and C5 are reversed in both solvents.