食物链种群模型的格子Boltzmann方法模拟

用格子Boltzmann方法求解用反应一扩散方程组描述的食物链种群模型．我们用一维和二维方程组进行数值实验,模拟结果与现有的数值实验结果很好地吻合,反映了格子Boltzmann方法的高效性和稳定性,并就二维格子、Boltzmann格式,通过其等价的差分格式,由极值原理证明了该格式的稳定性．     

Modeling of Nonlinear Chemical Reaction Systems and Two-Parameter Stochastic Resonance

The idea of stochastic resonance (SR) is extended to two-parameter dynamical systems based on the Oregonator model of the Belousov-Zhabotinsky (BZ) reaction. The first case presents the photosensitivity of the reaction, and light flux and a flow rate are the two control parameters. The second case presents the effect of temperature on the oscillatory behaviors, and temperature and a flow rate are the control parameters. Stochastic resonance is demonstrated in the first case in which a signal and noise are applied to the different inputs, respectively. The scenario and novel aspects of SR in two-parameter systems are discussed, and the possibility of the analogous SR in biological systems is also pointed out.     

Chemical Reaction Networks’ Programming for Solving Equations

The computational ability of the chemical reaction networks (CRNs) using DNA as the substrate has been verified previously. To solve more complex computational problems and perform the computational steps as expected, the practical design of the basic modules of calculation and the steps in the reactions have become the basic requirements for biomolecular computing. This paper presents a method for solving nonlinear equations in the CRNs with DNA as the substrate. We used the basic calculation module of the CRNs with a gateless structure to design discrete and analog algorithms and realized the nonlinear equations that could not be solved in the previous work, such as exponential, logarithmic, and simple triangle equations. The solution of the equation uses the transformation method, Taylor expansion, and Newton iteration method, and the simulation verified this through examples. We used and improved the basic calculation module of the CRN++ programming language, optimized the error in the basic module, and analyzed the error’s variation over time.     

Numerical Modelling of Electroosmotic Driven Flow in Nanoporous Media by Lattice Boltzmann Method

The lattice Boltzmann method was employed to simulate electroosmotic driven flow and Debye layer screening in conducting electrolyte around a porous structure with average size of 40 nm. The charge screening around the nanopores was investigated by solving the vector-superpositioned potential equilibrium distribution function and adding electro-kinetic force term to the evolution equation. In this intermediate case of moderate Debye length, the electrophoresis problem becomes complicated. The motion of the particles distorts the screening cloud, which becomes asymmetric, resulting in very complex interactions between the electrolyte, the screening cloud and the particle; but the Electroosmotic Flow (EOF) behaviour was still considered based on the Helmoholtz-Smoluchowski model with adaptation to fit nanoporous flow in the porous structure. In the present approach, the flow in the nanopores is directly modelled; the detailed flow information can be obtained by simplifying the repeated macrostructure. Due to the symmetry of the domain, the size of computational domain can be largely reduced by less repeated spherical nanoparticles. Each pore of the medium contains several lattice nodes on the simplified curved edges and potential gradients are produced by adjusting the zeta potential value. The velocity results for pressure-driven and EOF flows agree well with the analytical solutions and recent experimental results. In particular, the interface between solid particles and fluids, the influences of porosity, solid particle diameter, yield stress and electric parameters in EOF were investigated. The anti-adhesion effect of electroosmotic pumping effect was evaluated, and the pulsed DC was applied in order to enhance the performance of the electroosmotic pumping. The results demonstrate that the present lattice Boltzmann model is capable of modelling flow through nanoporous media at certain restrictions while some results deviate from the predictions based on the macroscopic theories.     

Numerical Study of Wetting Transitions on Biomimetic Surfaces Using a Lattice Boltzmann Approach with Large Density Ratio

The hydrophobicity of natural surfaces has drawn much attention of scientific communities in recent years.By mimicking natural surfaces,the manufactured biomimetic hydrophobic surfaces have been widely applied to green technologies such as self-cleaning surfaces.Although the theories for wetting and hydrophobicity have been developed,the mechanism of wetting transitions between heterogeneous wetting state and homogeneous wetting state is still not fully clarified.As understanding of wetting transitions is crucial for manufacturing a biomimetic superhydrophobic surface,more fundamental discussions in this area should be carried out.In the present work,the wetting transitions are numerically studied using a phase field lattice Boltzmann approach with large density ratio,which should be helpful in understanding the mechanism of wetting transitions.The dynamic wetting transition processes between Cassie-Baxter state and Wenzel state are presented,and the energy barrier and the gravity effect on transition are discussed.It is found that the two wetting transition processes are irreversible for specific inherent contact angles and have different transition routes,the energy barrier exists on an ideally patterned surface and the gravity can be crucial to overcome the energy barrier and trigger the transition.     

Phosphorylcholine Group-immobilized Surface Prepared on Polydimethylsiloxane Membrane by In Situ Reaction for Its Reduced Biofouling

To reduce interactions between biological molecules and the surface of microchip devices including the microchip, which should be conducted to improve sensitivity, reactivity, and the typical phospholipid polar group, the phosphorylcholine group-immobilized surfaces were prepared. The surface modification of polydimethylsiloxane (PDMS) was performed by in situ reaction during curing by cross-linking the PDMS prepolymers. Since it is known that 2-methacryloyloxyethyl phosphorylcholine (MPC) facilitates the preparation of biomedical polymers with excellent biocompatibility and antithrombogenicity, it was used as the reactant for surface modification. The MPC was coated on the glass substrate, and two-liquid-type PDMS prepolymers were then applied. During the curing process of the vinyl groups of poly(dimetylsiloxane-co-methylsiloxane) and poly(dimethylsiloxane-co-methylvinylsiloxane), the methacrylate group in MPC was attached onto the PDMS surface via a hydrosilyl group. Analysis of the surface characteristics by X-ray photoelectron spectroscopy and measurement of the surface contact angle revealed that the introduction of the phosphorylcholine group in the MPC unit on the surface induced hydrophilicity at the surface. Further, protein adsorption on the surface decreased with an increase in the number of phosphorylcholine groups. Based on these results, we concluded that the construction of the phosphorylcholine group-enriched surface on the PDMS substrate could be achieved by immobilization of MPC, and it may facilitate fabrication of biomedical devices, particularly microfluidic devices.     

响应面法优化脯氨酸羟化酶转化反应工艺条件

通过优化脯氨酸羟化酶表达条件和转化反应条件,提高其转化反应效率。采用单因素法筛选脯氨酸羟化酶的最佳诱导温度、诱导剂浓度和转化反应条件,并采用响应面法预测影响转化反应各因素的最佳条件。结果显示,经过筛选和验证,蛋白表达最适诱导温度为28℃,IPTG浓度为0.2 mmol/L;转化反应最佳条件为:120 mmol/L 2-(N-吗啡啉)乙磺酸(pH 6.6)、1.5% Nonidet P-40、200 mmol/L L-脯氨酸、200 mmol/L α-酮戊二酸,6 mmol/L L-抗坏血酸、6.0 mmol/L 硫酸亚铁,最适反应温度为27℃,振荡速率为152 r/min。在最佳条件下,转化反应进行48 h后产物反式-4-羟基-L-脯氨酸的转化率可达100%,为合成反式-4-羟基-L-脯氨酸奠定了坚实的实验基础。     

Computer Simulation of Surface Segregation

Abstract

Computer simulation techniques can now reliably model the surface structure and energies of inorganic solids. We present recent work which has been directed at modelling the segregation of impurities. The techniques are based on energy minimisation where the forces between the atoms are described by the Born model of solids. We initially show that magnesium and calcium segregation to the prism surfaces of alumina reproduce the available experimental data within the uncertainties of the experimental technique. However, reliable experimental data is not always available, and hence we show using the examples of calcium segregation to zirconia surfaces can give insights to the surface structure and provide predictions for experiment to test. Secondly, the simulations can be verified by comparison with morphologies. This is illustrated by comparison of the experimentally determined morphology of calcite with magnesium and lithium impurities with those calculated. Next extensions to the energy minimisation methods are described using dynamical techniques based on lattice and molecular dynamics. Finally, we describe the situation where there is phase separation and the structure and stability of the interface is governed by the epitaxial relations between the underlying oxide and the impurity oxide.     

A New Version of the Insertion Particle Method for Determining the Chemical Potential by Monte Carlo Simulation

A new version of the test particle method for determining the chemical potential by Monte Carlo simulations is proposed. The method, applicable to any fluid at any density, combines the Widom's test particle insertion method with the ideas of the scaled particle theory, gradual insertion method and multistage sampling. Its applicability is exemplified by evaluating the chemical potential of the hard sphere fluid at a very high density in semi-grand-canonical and grand-canonical ensembles. A theory estimating the efficiency (i.e. statistical errors) of the method is proposed and the results are compared with the Widom's and gradual insertion methods, and the analytic results.     

A Multisite Strategy for Enhancing the Hydrogen Evolution Reaction on a Nano‐Pd Surface in Alkaline Media

The hydrogen evolution reaction (HER) on a noble metal surface in alkaline media is more sluggish than that in acidic media due to the limited proton supply. To promote the reaction, it is necessary to transform the alkaline HER mechanism via a multisite catalyst, which has additional water dissociation sites to improve the proton supply to an optimal level. Here, this study reports a top‐down strategy to create a multisite HER catalyst on a nano‐Pd surface and how to further fine‐tune the areal ratio of the water dissociation component to the noble metal surface in core/shell‐structured nanoparticles (NPs). Starting with Pd/Fe₃O₄ core/shell NPs, electrochemical cycling is used to tune the coverage of iron (oxy)hydroxide on a Pd surface. The alkaline HER activity of the core/sell Pd/FeO_x (OH)_2?2x NPs exhibits a volcano‐shaped correlation with the surface Fe species coverage. This indicates an optimum coverage level where the rates of both the water dissociation step and the hydrogen formation step are balanced to achieve the highest efficiency. This multisite strategy assigns multiple reaction steps to different catalytic sites, and should also be extendable to other core/shell NPs to optimize their HER activity in alkaline media.     

DEM Numerical Simulation of Abrasive Wear Characteristics of a Bioinspired Ridged Surface

<正> This paper presents numerical investigations into a ridged surface whose design is inspired by the geometry of a Farrer'sscallop.The objective of the performed research is to assess if the proposed Bioinspired Ridged Surface (BRS) can potentiallyimprove wear resistance of soil-engaging components used in agricultural machinery and to validate numerical simulationsperformed using software based on the Discrete Element Method (DEM).The wear performance of the BRS is experimentallydetermined and also compared with a conventional flat surface.Different size of soil particles and relative velocities between theabrasive sand and the testing surfaces are used.Comparative results show that the numerical simulations are in agreement withthe experimental results and support the hypothesis that abrasive wear is greatly reduced by substituting a conventional flatsurface with the BRS.     

Simulation Modelling Study of Self-Assembled Nanoparticle Coatings for Retinal Implants

The electrode resolution of current retinal prostheses is still far from matching the densities of retinal neurons. Decreasing electrode diameter increases impedance levels thus deterring effective stimulation of neurons. One solution is to increase the surface roughness of electrodes, which can be done via nanoparticle coatings. This paper explores a Lattice Gas Model of the drying-mediated self-assembly of nanoparticle mixtures. The model includes representations for different types of nanoparticles, solvent, vapour, substrate and the energetic relationships between these elements. The dynamical aspect of the model is determined by energy minimization, stochastic fluctuations and physical constraints. The model attempts to unravel the relationships between different experimental conditions (e.g. evaporation rate, substrate characteristics and solvent viscosity) and the surface roughness of resulting assemblies. Some of the main results include the facts that the assemblies formed by nanoparticles of different sizes can boost roughness in specific circumstances and that the optimized assemblies can exhibit walled or stalagmite structures. This study provides a set of simulation modelling experiments that if confirmed in the laboratory may result in new and useful materials.     

Chemical Synthesis of Human β-Defensin (hBD)-1, -2, -3 and -4: Optimization of the Oxidative Folding Reaction

Reduced human β-defensin (hBD)-1, -2, -3 and -4 synthesized by Boc chemistry were subjected to oxidative folding reaction under optimal conditions. Among the factors affecting the oxidative folding in the presence of reduced and oxidized glutathione (GSH/GSSG), the buffer concentration and reaction temperature were essential for the predominant formation of the native disulfide structure. The homogeneity of the four synthetic hBDs was confirmed by analytical procedures using RP-HPLC, IEX-HPLC, capillary zone electrophoresis (CZE) and MALDI-TOF MS as well as sequencing, although high temperature (70 °C) was used for the RP-HPLC analysis of hBD-3 and hBD-4 to exclude the influence of equilibrium with the respective conformers having native disulfide pairing. All synthetic hBDs were shown to possess the native disulfide structure by sequential analyses and mass measurements with cystine segments obtained by enzymatic digestion. Upon digestion of hBD-1 and hBD-4 with proline specific endopeptidase, the Cys-X bond was found to be reproducibly cleaved together with the Pro-X bond although the cleavage of Cys-X afforded the appropriate cystine segments for determining the disulfide structure of hBD-1 and hBD-4. With respect to antimicrobial activity against E. coli, the four synthetic hBDs of high homogeneity possessed the same potencies as those reported previously.Australian Peptide Conference Issue     

太阳能电池反应模拟光合系统反应中心电荷复合形成三线态分子的过程

光合系统反应中心普遍存在电荷复合反应形成三线态分子的过程,并通过所形成的三线态β-胡萝卜素将剩余的能量经无辐射通道耗散给环境,实现光合系统的光保护功能.这一过程在人工合成系统中十分罕见,见诸报道的仅有少数由给体-受体组成的超分子体系.首次报道应用染料敏化TiO2胶体颗粒的人工太阳能电池反应,模拟光合系统三线态分子的形成过程,成功地观测到了视黄酸自由基正离子与TiO2表面束缚电子复合而形成的三线态视黄酸分子,并对其光谱和动力学过程进行了纳秒时间分辨光谱表征.     

Computational Phlebology: The Simulation of a Vein Valve

We present a three-dimensional computer simulation of the dynamics of a vein valve. In particular, we couple the solid mechanics of the vein wall and valve leaflets with the fluid dynamics of the blood flow in the valve. Our model captures the unidirectional nature of blood flow in vein valves; blood is allowed to flow proximally back to the heart, while retrograde blood flow is prohibited through the occlusion of the vein by the valve cusps. Furthermore, we investigate the dynamics of the valve opening area and the blood flow rate through the valve, gaining new insights into the physics of vein valve operation. It is anticipated that through computer simulations we can help raise our understanding of venous hemodynamics and various forms of venous dysfunction.     

Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson‐Boltzmann approach

The ion atmosphere created by monovalent (Na⁺) or divalent (Mg²⁺) cations surrounding a B‐form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson‐Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and two‐dimensional cation concentrations and by calculating the total number of cations and net solution charge surrounding the DNA. Na⁺ ion distributions near the DNA were more diffuse in PB calculations than in corresponding MD simulations, with PB calculations predicting lower concentrations near DNA groove sites and phosphate groups and a higher concentration in the region between these locations. Other than this difference, the Na⁺ distributions generated by the two methods largely agreed, as both predicted similar locations of high Na⁺ concentration and nearly identical values of the number of cations and the net solution charge at all distances from the DNA. In contrast, there was greater disagreement between the two methods for Mg²⁺ cation concentration profiles, as both the locations and magnitudes of peaks in Mg²⁺ concentration were different. Despite experimental and simulation observations that Mg²⁺ typically maintains its first solvation shell when interacting with nucleic acids, modeling Mg²⁺ as an unsolvated ion during PB calculations improved the agreement of the Mg²⁺ ion atmosphere predicted by the two methods and allowed for values of the number of bound ions and net solution charge surrounding the DNA from PB calculations that approached the values observed in MD simulations. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 834–848, 2014.     

红松应力木木材形成组织的化学组成特征分析

检测分析了天然红松应力木木材形成组织的乙酰溴木质素含量,傅里叶变换红外光谱和X射线衍射图谱。结果表明：木材形成组织木质素含量小于成熟木材,应压木中木质素含量高于正常材;木材形成组织中羟基特征峰的位置有异于成熟木材,在波数1 034~1 510 cm^-1处的吸收峰有明显差异,化学官能团的相对吸收强度低于成熟木材;应压木木材形成组织红外光谱特征峰的位置和峰形与对应木、正常木的基本相同;应压木全谱图各化学官能团的相对吸收强度大于正常木。木材形成组织X射线衍射强度低于成熟木材,应压木低于正常材和对应木;木材形成组织纤维素相对结晶度小于成熟木材,应压木低于正常材和对应木。说明木材形成过程中组织的化学特征是动态变化的。应力木形成中木材组织化学特征就与正常木有差异。     

Performance Simulation of Cluster-Based Asynchronous Soft Real-Time Systems

In this paper, we present a model designed for interactive simulation of cluster-based asynchronous soft real-time systems such as the Jambala platform of Ericsson. To build the simulator, we selected PlasmaCORE – Ericsson's proprietary simulation framework that supports a wide range of run-time modifications to the simulated system. Based on this choice, the information model of the system was developed and a prototype tool was implemented. We describe the essential features of the model and subsequently, we demonstrate the feasibility of the tool by presenting the benchmark results that compare the model-based simulation results with measurements taken on a real Jambala cluster. The flexibility of the simulation tool is demonstrated on a number of what-if scenarios that also pinpoint some important features of such clusters.     

利用表面等离子体共振仪检测黄瓜花叶病毒

目的：研究一种便捷、高效地检测黄瓜花叶病毒（CMV）的方法。方法：利用表面等离子体共振（SPR）技术检测CMV。首先用11-MUA修饰SPR金片,再用EDC／NHS活化,之后通过NHS酯基与CMV抗体结合,用BSA封闭未结合的NHS酯基。将SPR金片装入SPR仪,通入待检样品,通过折射率变化实时监测实验过程。结果：该方法检测CMV的灵敏度能够达到10ng／mL,具有良好的特异性,与同属的花生矮化病毒、番茄不孕病毒无交叉反应。结论：建立的SPR方法操作简单、灵敏度高、特异性好,是一种新的高效检测CMV的方法。