Total Chemical Synthesis of Biologically Active Fluorescent Dye‐Labeled Ts1 Toxin

Ts1 toxin is a protein found in the venom of the Brazilian scorpion Tityus serrulatus. Ts1 binds to the domain II voltage sensor in the voltage‐gated sodium channel Nav and modifies its voltage dependence. In the work reported here, we established an efficient total chemical synthesis of the Ts1 protein using modern chemical ligation methods and demonstrated that it was fully active in modifying the voltage dependence of the rat skeletal muscle voltage‐gated sodium channel rNav1.4 expressed in oocytes. Total synthesis combined with click chemistry was used to label the Ts1 protein molecule with the fluorescent dyes Alexa‐Fluor 488 and Bodipy. Dye‐labeled Ts1 proteins retained their optical properties and bound to and modified the voltage dependence of the sodium channel Nav. Because of the highly specific binding of Ts1 toxin to Nav, successful chemical synthesis and labeling of Ts1 toxin provides an important tool for biophysical studies, histochemical studies, and opto‐pharmacological studies of the Nav protein.     

A size-modified poisson–boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel

We present a new size-modified Poisson–Boltzmann ion channel (SMPBIC) model and use it to calculate the electrostatic potential, ionic concentrations, and electrostatic solvation free energy for a voltage-dependent anion channel (VDAC) on a biological membrane in a solution mixture of multiple ionic species. In particular, the new SMPBIC model adopts a membrane surface charge density and a natural Neumann boundary condition to reflect the charge effect of the membrane on the electrostatics of VDAC. To avoid the singularity difficulties caused by the atomic charges of VDAC, the new SMPBIC model is split into three submodels such that the solution of one of the submodels is obtained analytically and contains all the singularity points of the SMPBIC model. The other two submodels are then solved numerically much more efficiently than the original SMPBIC model. As an application of this SMPBIC submodel partitioning scheme, we derive a new formula for computing the electrostatic solvation free energy. Numerical results for a human VDAC isoform 1 (hVDAC1) in three different salt solutions, each with up to five different ionic species, confirm the significant effects of membrane surface charges on both the electrostatics and ionic concentrations. The results also show that the new SMPBIC model can describe well the anion selectivity property of hVDAC1, and that the new electrostatic solvation free energy formula can significantly improve the accuracy of the currently used formula. © 2019 Wiley Periodicals, Inc.     

Simulating ion channel activation mechanisms using swarms of trajectories

Atomic-level studies of protein activity represent a significant challenge as a result of the complexity of conformational changes occurring on wide-ranging timescales, often greatly exceeding that of even the longest simulations. A prime example is the elucidation of protein allosteric mechanisms, where localized perturbations transmit throughout a large macromolecule to generate a response signal. For example, the conversion of chemical to electrical signals during synaptic neurotransmission in the brain is achieved by specialized membrane proteins called pentameric ligand-gated ion channels. Here, the binding of a neurotransmitter results in a global conformational change to open an ion-conducting pore across the nerve cell membrane. X-ray crystallography has produced static structures of the open and closed states of the proton-gated GLIC pentameric ligand-gated ion channel protein, allowing for atomistic simulations that can uncover changes related to activation. We discuss a range of enhanced sampling approaches that could be used to explore activation mechanisms. In particular, we describe recent application of an atomistic string method, based on Roux's “swarms of trajectories” approach, to elucidate the sequence and interdependence of conformational changes during activation. We illustrate how this can be combined with transition analysis and Brownian dynamics to extract thermodynamic and kinetic information, leading to understanding of what controls ion channel function. © 2019 Wiley Periodicals, Inc.     

Polycaprolactone solution–based ink for designing microfluidic channels on paper via 3D printing platform for biosensing application

This work reports a novel fabrication technique for development of channels on paper‐based microfluidic devices using the syringe module of a 3D printing syringe–based system. In this study, printing using polycaprolactone (PCL)‐based ink (Mw 70 000‐90 000) was employed for the generation of functional hydrophobic barriers on Whatman qualitative filter paper grade 1 (approximate thickness of 180 μm and pore diameter of 11 μm), which would effectively channelize fluid flow to multiple assay zones dedicated for different analyte detection on a microfluidic paper‐based analytical device (μPAD). The standardization studies reveal that a functional hydrophilic channel for sample conduction fabricated using the reported technique can be as narrow as 460.7 ± 20 μm and a functional hydrophobic barrier can be of any width with a lower limit of about 982.2 ± 142.75 μm when a minimum number of two layers of the ink is extruded onto paper. A comparison with the hydrodynamic model established for writing with ink is used to explain the width of the line printed by this system. A fluid flow analysis through a single channel system was also carried out to establish its conformity with the Washburn model, which governs the fluid flow in two‐dimensional μPAD. The presented fabrication technique proves to be a robust strategy that effectively taps the advantages of this 3D printing technique in the production of μPADs with enhanced speed and reproducibility.     

Si(111) Electrode/Electrolyte Interracial Studied by in-situ Second Harmonic Generation

Si(111) electrode has been widely used in electrochemical and photoelectrochemical studies. The potential dependent measurements of the second harmonic generation (SHG) were performed to study Si(111) electrode interface. At different azimuthal angles of the Si(111) and under different polarization combinations, the curve of the intensity of SHG with extern potential has a different form of line or parabola. Quantitative analysis showed that these differences in the potential-dependence can be explained by the isotropic and anisotropic contribution of the Si(111) electrode. The change in the isotropic and anisotropic contribution of the Si(111) electrode may be attributed to the increase in the doping concentration of Si(111) electrodes.     

超声波燃气表矩形流道的雷诺修正系数仿真研究

在超声波流量计测量技术中, 雷诺修正系数相关的研究对于提高计量精度有重要作用. 为研究矩形流道的雷诺修正系数与雷诺数的关系, 对矩形流道在常温常压流量较小情况下进行仿真, 结果发现: 矩形流道层流状态下的雷诺修正系数与雷诺数呈线性相关. 保持压强、体积流量不变, 在不同温度下进行仿真及拟合, 结果表明: 在不同温度下雷诺修正系数与雷诺数的线性关系依然满足. 在上述实验基础上, 对矩形流道湍流状态下的雷诺修正系数与雷诺数关系进行研究, 通过改变温度、压强和体积流量进行仿真及拟合发现, 矩形流道湍流状态下雷诺修正系数与雷诺数呈非线性相关.     

光学相干控制中脉冲光束等相面的实时测控

描述了飞秒脉冲基频光、倍频光光束位相差对相干控制光电流注入的控制作用,提出一种控制基频光、倍频光在全光孔径干涉光场内的等相面保持一致的实验方案,制作了一套相位差稳定自动控制系统,并应用于光学相干控制光电流实验中,获得较好的实时控制结果.     

基于光子晶体的三端口分插复用器

提出了一种新的基于对称全反射壁的光子晶体分插复用器,与其他类型的光子晶体复用器相比,无需对介质柱进行复杂的调节即可实现100%上/下载,方便实际制造.提出的理论模型与基于二维时域有限差分(FDTD)法的数值实验相当吻合,显示出这种器件具有优良的上/下载性能.     

Hydrodynamic instability of premixed flame propagating in narrow planar channel in the presence of gas flow

The paper analyses the hydrodynamic instability of a flame propagating in the space between two parallel plates in the presence of gas flow. The linear analysis was performed in the framework of a two-dimensional model that describes the averaged gas flow in the space between the plates and the perturbations development of two-dimensional combustion wave. The model includes the parametric dependences of the flame front propagation velocity on its local curvature and on the combustible gas velocity averaged along the height of the channel. It is assumed that the viscous gas flow changes the surface area of the flame front and thereby affects the propagation velocity of the two-dimensional combustion wave. In the absence of the influence of the channel walls on the gas flow, the model transforms into the Darrieus–Landau model of flame hydrodynamic instability. The dependences of the instability growth rate on the wave vector of disturbances, the velocity of the unperturbed gas flow, the viscous friction coefficients and other parameters of the problem are obtained. It is shown that the viscous gas flow in the channel can lead, in some cases, to a significant increase in instability compared with a flame propagating in free space. In particular, the instability increment depends on the direction of the gas flow with respect direction of the flame propagation. In the case when the gas flow moves in the opposite direction to the direction of the flame propagation, the pulsating instability can appear.     

Channel-Supermodular Entropies: Order Theory and an Application to Query Anonymization

This work introduces channel-supermodular entropies, a subset of quasi-concave entropies. Channel-supermodularity is a property shared by some of the most commonly used entropies in the literature, including Arimoto–Rényi conditional entropies (which include Shannon and min-entropy as special cases), k-tries entropies, and guessing entropy. Based on channel-supermodularity, new preorders for channels that strictly include degradedness and inclusion (or Shannon ordering) are defined, and these preorders are shown to provide a sufficient condition for the more-capable and capacity ordering, not only for Shannon entropy but also regarding analogous concepts for other entropy measures. The theory developed is then applied in the context of query anonymization. We introduce a greedy algorithm based on channel-supermodularity for query anonymization and prove its optimality, in terms of information leakage, for all symmetric channel-supermodular entropies.