Development of an improved divergence‐free‐condition compensated coupled framework to solve flow problems with time‐varying geometries

In this article a coupled version of the improved divergence‐free‐condition compensated method will be proposed to simulate time‐varying geometries by direct forcing immersed boundary method. The proposed method can be seen as a quasi‐multi‐moment framework due to the fact that the momentum equations are discretized by both cell‐centered and cell‐face velocity. For simulating time‐varying geometries, a semi‐implicit iterative method is proposed for calculating the direct forcing terms. Treatments for suppressing spurious force oscillations, calculating drag/lift forces, and evaluating velocity and pressure for freshly cells will also be addressed. In order to show the applicability and accuracy, analytical as well as benchmark problems will be investigated by the present framework and compared with other numerical and experimental results.     

Nonlinear elastic constitutive relations of residually stressed composites with stiff curved fibres

Applied Mathematics and Mechanics - Mechanical models of residually stressed fibre-reinforced solids, which do not resist bending, have been developed in the literature. However, in some residually...     

紫色球杆菌视紫红质光谱特性的机器学习研究

近年来，机器学习等人工智能技术被应用于蛋白质工程，其在蛋白质结构、功能预测、催化活性等研究中具有独特优势。在未知蛋白质结构的情况下，将蛋白质序列和功能特性与机器学习相结合，基于序列-活性关系（innovative sequence-activity relationship，ISAR）算法，将蛋白质氨基酸序列数字化，用快速傅里叶变换（fast four transform，FFT）进行预处理，再进行偏最小二乘回归建模，可在数据集较少情况下拟合得到最佳模型。通过机器学习对紫色球杆菌视紫红质（gloeobacter violaceus rhodopsin，GR）的突变体蛋白质氨基酸序列与光谱最大吸收波长进行建模，获得了最佳模型。用最佳索引LEVM760106建模得到的确定系数R² 为0.944，均方误差E为11.64。用小波变换进行的预处理，其R² 虽也约为0.944，但E大于11.64，不及FFT进行的预处理。方法较好地解决了蛋白质序列与功能特性之间的数学建模问题，在蛋白质工程中可为预测更优的突变体提供支持。     

Structured water chains in external electric fields

ABSTRACT

We study the structural, energetic and electronic properties of the structured water chain clusters within the density functional theory. We refer the structured water chains to those water clusters that have specific geometric patterns stretched along one direction. External electric field required to keep the structures open chain, thereby preventing them to form closed structures, is applied along the length of the chain. The structures are essentially periodic with basic repeating unit consisting of the corner- or edge-sharing 4-, 5- or 6-membered ring water clusters. Our calculations underscore the possible existence of such structured water clusters in the electrostatic environments, which we simulate in its simplicity employing a dipolar, uniform and static electric field. Analysis reveals that the 5-membered ring water chain clusters, i.e. the pentamer chain clusters have the lowest average dipole moment per water molecule while the threshold field, that marks the onset of the field-induced closure of the HOMO (highest occupied molecular orbital)-LUMO (lowest unoccupied molecular orbital) energy gap, is highest, followed by that for the tetramer and hexamer chains. The results suggest that the pentamer chains are the most stable clusters over a wide range of electric fields.     

The structural,electronic and magnetic properties of Ag4M and Ag4MCO (M = Sc–Zn) clusters

The structures, spectra and electronic and magnetic properties of Ag₄M and Ag₄MCO (M?=?Sc–Zn) clusters have been studied using density functional theory and CALYPSO structure searching method. Structural searches show that M atoms except Zn tend to occupy the highest coordination position in the ground state Ag₄M and Ag₄MCO clusters. Carbon monoxide is most easily adsorbed on Ag atom of Ag₄Zn and M atom of other Ag₄M. Infrared and Raman spectra, photoabsorption spectra and photoelectron spectra of Ag₄M and Ag₄MCO clusters are forecasted and can be used to identify these clusters from experiment. Analysis of electronic properties indicates that the adsorption of CO on Ag₄M clusters changes the zero vibrational energy (ZPVE) and increases stability of the host clusters. Dopant atoms except for Zn improve the stability of silver cluster. The Ag₄Ni cluster shows high chemical activity and maximum adsorption energy for carbon monoxide. Magnetism calculations reveal that the magnetic moment of Ag₄M (M?=?Mn–Ni) cluster adsorbed by carbon monoxide is decreased by 2 μ_B. The change of magnetic moment makes it possible to be used as a nanomaterial for carbon monoxide detection. Simultaneously, it is found that the adsorption of CO on Ag₄Cu cluster is a physical adsorption.     

More efficient time integration for Fourier pseudospectral DNS of incompressible turbulence

Time integration of Fourier pseudospectral DNS is usually performed using the classical fourth-order accurate Runge-Kutta method or other second- or third-order methods, with a fixed step size. We investigate the use of higher-order Runge-Kutta pairs and automatic step size control based on local error estimation. We find that the fifth-order accurate Runge-Kutta pair of Bogacki and Shampine gives much greater accuracy at a significantly reduced computational cost. Specifically, we demonstrate speedups of 2× to 10× for the same accuracy. Numerical tests (including the Taylor-Green vortex, Rayleigh-Taylor instability, and homogeneous isotropic turbulence) confirm the reliability and efficiency of the method. We also show that adaptive time stepping provides a significant computational advantage for some problems (like the development of a Rayleigh-Taylor instability) without compromising accuracy.     

A giant enhancement of magnetic moment in a ternary three-shell icosahedral cluster: Fe@Mn12@Au20

ABSTRACT

The average magnetic moment per atom of Mn₁₃ cluster is expected to be enhanced by doping or coating with a shell. Several ternary core–shell icosahedral clusters TM@Mn₁₂@Au₂₀ were constructed by combining substituting the central Mn with VIII elements (Fe, Co, Ni, Ru, Rh, Pd and Pt) and coating with a icosahedral Au₂₀ shell, and systematically studied by using the first-principles density functional method. Compared to Mn₁₃, Fe@Mn₁₂@Au₂₀ cluster shows a giant enhancement on total magnetic moment (52?µ_B) which can be greatly attributed to the ferromagnetic coupling between spin moments of atoms. Coating with Au₂₀ shell enlarged the average distances of TM-Mn and Mn-Mn and is a useful way to change the magnetic coupling style. By analysis of density of states and electron localisation functional, we can conclude that the weak hybridisation between Fe and Mn in Fe@Mn₁₂@Au₂₀ is propitious to maintain their original direction of spin moments of atoms and then form ferromagnetic coupling.     

Spectral estimates for saddle point matrices arising in weak constraint four‐dimensional variational data assimilation

We consider the large sparse symmetric linear systems of equations that arise in the solution of weak constraint four‐dimensional variational data assimilation, a method of high interest for numerical weather prediction. These systems can be written as saddle point systems with a 3 × 3 block structure but block eliminations can be performed to reduce them to saddle point systems with a 2 × 2 block structure, or further to symmetric positive definite systems. In this article, we analyse how sensitive the spectra of these matrices are to the number of observations of the underlying dynamical system. We also obtain bounds on the eigenvalues of the matrices. Numerical experiments are used to confirm the theoretical analysis and bounds.     

A molecular fluorophore in citric acid/ethylenediamine carbon dots identified and quantified by multinuclear solid-state nuclear magnetic resonance

The composition of fluorescent polymer nanoparticles, commonly referred to as carbon dots, synthesized by microwave-assisted reaction of citric acid and ethylenediamine was investigated by ¹³C, ¹³C{¹H}, ¹H─¹³C, ¹³C{¹⁴N}, and ¹⁵N solid-state nuclear magnetic resonance (NMR) experiments. ¹³C NMR with spectral editing provided no evidence for significant condensed aromatic or diamondoid carbon phases. ¹⁵N NMR showed that the nanoparticle matrix has been polymerized by amide and some imide formation. Five small, resolved ¹³C NMR peaks, including an unusual ═CH signal at 84 ppm (¹H chemical shift of 5.8 ppm) and ═CN₂ at 155 ppm, and two distinctive ¹⁵N NMR resonances near 80 and 160 ppm proved the presence of 5-oxo-1,2,3,5-tetrahydroimidazo[1,2-a]pyridine-7-carboxylic acid (IPCA) or its derivatives. This molecular fluorophore with conjugated double bonds, formed by a double cyclization reaction of citric acid and ethylenediamine as first shown by Y. Song, B. Yang, and coworkers in 2015, accounts for the fluorescence of the carbon dots. Cross-peaks in a ¹H─¹³C HETCOR spectrum with brief ¹H spin diffusion proved that IPCA is finely dispersed in the polyamide matrix. From quantitative ¹³C and ¹⁵N NMR spectra, a high concentration (18 ± 2 wt%) of IPCA in the carbon dots was determined. A pronounced gradient in ¹³C chemical-shift perturbations and peak widths, with the broadest lines near the COO group of IPCA, indicated at least partial transformation of the carboxylic acid of IPCA by amide or ester formation.