ReaxFF MD局部区域反应追踪与物理性质可视化分析

Recently, the application of ReaxFF based reactive molecular dynamics simulation (ReaxFF MD) in complex processes of pyrolysis, oxidation and catalysis has attracted considerable attention. The analysis of the simulation results of these processes is challenging owing to the complex chemical reactions involved, coupled with their dynamic physical properties. VARxMD is a leading tool for the chemical reaction analysis and visualization of ReaxFF MD simulations, which allows the automated analysis of reaction sites to get overall reaction lists, evolution trends of reactants and products, and reaction networks of specified reactants and products. The visualization of the reaction details and dynamic evolution profiles are readily available for each reactant and product. Additionally, the detailed reaction sites of bond breaking and formation are available in 2D chemical structure diagrams and 3D structure views; for specified reactions, they are categorized on the basis of the chemical structures of the bonding sites or function groups in the reacting species. However, the current VARxMD code mainly focuses on global chemical reaction information in the simulation system of the ReaxFF MD, and is incapable of locally tracking the chemical reaction and physical properties in a 3D picked zone. This work extends the VARxMD from global analysis to a focused 3D zone picked interactively from the 3D visualization modules of VARxMD, as well as physical property analysis to complement reaction analysis. The analysis of reactions and physical properties can be implemented in three steps: picking and drawing a 3D zone, identifying molecules in the picked zone, and analyzing the reactions and physical properties of the picked molecules. A 3D zone can be picked by specifying the geometric parameters or drawing on a screen using a mouse. The picking of a cuboid or sphere was implemented using the VTK 3D view libraries by specifying geometric parameters. The interactive 3D zone picking was implemented using a combination of observer and command patterns in the VTK visualization paradigm. The chemical reaction tracking and dynamic radial distribution function (RDF) of the 3D picked zone was efficiently implemented by inheriting data obtained from the global analysis of VARxMD. The reaction tracking between coal particles in coal pyrolysis simulation and dynamic structure characterization of carbon rich cluster formation in the thermal decomposition of an energetic material are presented as application examples. The obtained detailed reactions between the coal particles and comparison of the reaction between the locally and globally picked areas in the cuboid are helpful in understanding the role of micro pores in coal particles. The carbon to carbon RDF analysis and comparison of the spherical region picked for the layered molecular clusters in the pyrolysis system of the TNT crystal model with the standard RDF of the 5-layer graphene demonstrate the extended VARxMD as a chemical structure characteristic tool for detecting the dynamic formation profile of carbon rich clusters in the pyrolysis of TNT. The extended capability of VARxMD for a 3D picked zone of a ReaxFF MD simulation system can be useful for interfacial reaction analysis in a catalysis system, hot spot formation analysis in the detonation of energetic material systems, and particularly the pyrolysis or oxidation processes of coal, biomass, polymers, hydrocarbon fuels, and energetic materials.     

Group-Wise Principal Component Analysis for Exploratory Data Analysis

In this article, we propose a new framework for matrix factorization based on principal component analysis (PCA) where sparsity is imposed. The structure to impose sparsity is defined in terms of groups of correlated variables found in correlation matrices or maps. The framework is based on three new contributions: an algorithm to identify the groups of variables in correlation maps, a visualization for the resulting groups, and a matrix factorization. Together with a method to compute correlation maps with minimum noise level, referred to as missing-data for exploratory data analysis (MEDA), these three contributions constitute a complete matrix factorization framework. Two real examples are used to illustrate the approach and compare it with PCA, sparse PCA, and structured sparse PCA. Supplementary materials for this article are available online.     

Visualization of pool boiling on enhanced surfaces

This work reports experiments to visualize nucleate boiling on an enhanced tubular surface having sub-surface tunnels and surface pores. The finned copper tube had 1575 fins/m (40 fins/in.) and 0.8 mm fin height. The fins are covered by a thin foil sheet having 0.23 mm pores at 1.5 mm pore pitch along each interfin region. Data are provided for two foil cover sheets, one copper and the other a transparent plastic. The uniqueness of this work is that the visualization method allowed direct observation of the boiling process in the subsurface tunnels. Use of a high speed camera with 30 × magnification allowed detailed observation of the evaporation process in the tunnels and of the vapor bubbles emerging from the pores. The experiments were conducted for saturated and subcooled boiling in the horizontal and vertical orientations. For the vertical tube, the saturated boiling experiments showed that all of the tunnels were vapor filled except for liquid menisci in the corners. This was also true for the horizontal tube at high heat flux. For the horizontal tube at low heat flux, portions of the tunnel length was liquid filled. A large portion (70–90%) of the region was vapor filled except for liquid menisci in the corners, and the remaining part of the region had oscillating menisci. These experiments provide conclusive proof that the heat transfer mechanism in the subsurface tunnels is evaporation on the menisci in the corners.     

PIV measurement of the vertical cross-flow structure over tube bundles

Shell and tube heat exchangers are among the most commonly used types of heat exchangers. Shell-side cross-flow in tube bundles has received considerable attention and has been investigated extensively. However, the microscopic flow structure including velocity distribution, wake, and turbulent structure in the tube bundles needs to be determined for more effective designs. Therefore, in this study, in order to clarify the detailed structure of cross-flow in tube bundles with particle image velocimetry (PIV), experiments were conducted using two types of model; in-line and staggered bundles with a pitch-to-diameter ratio of 1.5, containing 20 rows of five 15 mm O.D. tubes in each row. The velocity data in the whole flow field were measured successfully by adjusting the refractive index of the working fluid to that of the tube material. The flow features were characterized in different tube bundles with regards to the velocity vector field, vortex structure, and turbulent intensity.     

Experimental study on the magnetic convection in a vertical cylinder

The flow of paramagnetic fluid inside a cylinder placed in a bore of a superconducting magnet was studied experimentally. Single-phase closed thermosyphon configuration was employed. The lower side wall of the cylindrical enclosure was heated while the upper side wall was cooled with the thin adiabatic interface in between. The experiment was carried out with an aqueous solution of glycerol. The magnetic susceptibility of the working fluid was increased by adding Gd(NO₃)₃ × 6H₂O and was measured by a magnetic susceptibility balance. The encapsulated liquid crystal slurry (KWN-2025, Japan Capsular Product Inc.) dispersed in the working fluid was illuminated in the middle height horizontal cross-section of the enclosure to visualize the temperature field. The color images of flow mode were taken by a digital camera. The average heat transfer rates were also measured. Depending on the Rayleigh number, different spoke patterns were observed. The number of angular structures (spokes) increased with increase not only in the Rayleigh number but also in the strength of magnetic field. The heated fluid was repelled by the magnetic field, while the cooled fluid was attracted. The magnetic field enhanced the heat transfer rate.     

Experimental study of turbulent round jet flow impinging on a square cylinder laid on a flat plate

A turbulent axisymmetric air jet impinging on a square cylinder mounted on a flat plate has been studied experimentally. Turbulence statistics and flow’s topology were investigated. When the surface was heated through uniform heat flux, local heat transfer coefficient was measured. The jet from a long round pipe, 75 pipe diameters (D) in length, at Reynolds number of 23,000, impinged vertically on the square cylinder (3D × 3D × 43D). Measurements were performed using particle image velocimetry, flow visualization using fluorescent dye and infrared thermography. The flow’s topology demonstrated a three-dimensional recirculation after separating from the square cylinder and a presence of foci between the bottom corner and the recirculation’s detachment line. The distribution of heat transfer coefficient was explained by the influence of these flow’s structures and the advection of kinetic energy. On the impingement wall of the square cylinder, a secondary peak in heat transfer coefficient was observed. Its origin can be attributed to very pronounced shear production coupled with the external turbulence coming from the free jet.     

Transversal vibrations of double-plate systems

This paper presents an analytical and numerical analysis of free and forced transversal vibrations of an elastically connected double-plate system. Analytical solutions of a system of coupled partial differential equations, which describe corresponding dynamical free and forced processes, are obtained using Bernoulli’s particular integral and Lagrange’s method of variation constants. It is shown that one-mode vibrations correspond to two-frequency regime for free vibrations induced by initial conditions and to three-frequency regime for forced vibrations induced by one-frequency external excitation and corresponding initial conditions. The analytical solutions show that the elastic connection between plates leads to the appearance of two-frequency regime of time function, which corresponds to one eigenamplitude function of one mode, and also that the time functions of different vibration modes are uncoupled, for each shape of vibrations. It has been proven that for both elastically connected plates, for every pair of m and n, two possibilities for appearance of the resonance dynamical states, as well as for appearance of the dynamical absorption, are present. Using the MathCad program, the corresponding visualizations of the characteristic forms of the plate middle surfaces through time are presented.The English text was polished by Keren Wang.     

A lysosomal polarity-specific two-photon fluorescent probe for visualization of autophagy

Autophagy plays a vital role in maintaining the balance of normal physiological state of living cells. In this paper, a polarity-specific two-photon fluorescent probe Lyso-NA based on naphthalimide was synthesized for the purpose of monitoring autophagy during biological research. The results of photophysical properties and theoretical calculation confirmed that different polarities of solvents mainly effected fluorescent intensities of probe. Fluorescent intensity, quantum yield and fluorescence lifetime of probe kept a good linear relationship with polarity respectively. In addition, due to its low toxicity and selective accumulation in lysosomes, Lyso-NA is suitable for detecting changes in lysosomal polarity of living cells. Compare with the imaging results of plasmid transfection, a better performed real-time long-term fluorescent visualization of autophagy in living cells was achieved. Probe Lyso-NA can work as an efficient and cost effective imaging tool for visualizing autophagy in living cells.     

Spatially-resolved measurement on time-dependent electromagnetic behavior in alternating current carrying coated conductor

Establishment of processing technology for multifilamentary coated conductors (CCs) is a key issue for superconducting electric power applications from the viewpoint of AC loss reduction. On the other hand, CCs sometimes have local inhomogeneity in the superconducting layers, and that will cause a current blocking in a filament or inhomogeneity of critical current among filaments in a multifilamentary CC. Therefore, we need an assessment method for local electromagnetic behavior on AC loss properties of CCs. In this study, we developed a method for visualizing time-dependent AC loss distribution in CCs by using scanning Hall probe microscopy. We succeeded in visualizing local current density, electric field and loss density simultaneously with a spatial resolution of a few hundred micrometers. The measurement system has possible scanning area of 150 × 50 mm² and current capacity of 500 A. This enables us to discuss the local electromagnetic behavior on a practical scale of CCs. We believe that this visualization method will be a very powerful tool to estimate the feasibility of processing technology for multifilamentary CCs.     

Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes

利用三种方法可视化化了Ru(II) ammine的金属到配体的电荷转移. 首先原子分辨的态密度显示HOMO上的密度主要在Ru上,LUMO 上的态密度在ammine上,这说明Ru上激发的电子会转移到ammine配体上. 第二,电荷差异密度揭示了所有的空穴都在Ru上,所有的电子都在ammine上. 第三,跃迁密度矩阵揭示了Ru和ammine上的电子空穴对的相关性. 这三种方法也用来研究Os(bpy)₂(p0p)Cl的金属到配体的电荷转移和Alq3配体到配体的电荷转移.