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.     

Enhanced multi‐objective optimization of a dimpled channel through evolutionary algorithms and multiple surrogate methods

Using a multi‐objective evolutionary algorithm (MOEA) and enhanced surrogate approximations, the present study demonstrates the numerical analysis and optimization of staggered‐dimple channels. Two surrogates, the response surface approximation (RSA) model and the Kriging (KRG) model, are applied in light of the surrogate fidelity of the approximate analysis. An enhanced Pareto‐optimal front is obtained by performing local resampling of the Pareto‐optimal front, which provides relatively more accurate Pareto‐optimal solutions in the design space for each surrogate model. Three dimensionless design variables are selected, which are related to geometric parameters, namely, the channel height, dimple print diameter, dimple spacing, and dimple depth. Two objective functions are selected that are related to the heat transfer and pressure loss, respectively. The objective‐function values are numerically evaluated through Reynolds‐averaged Navier–Stokes analysis at the design points that are selected through the Latin hypercube sampling method. Using these numerical simulations two surrogates, viz, the RSA and Kriging models, are constructed for each objective function and a hybrid MOEA is applied to obtain the Pareto‐optimal front. For the particular implementation of surrogate models, it is observed that Pareto‐optimal predictions of the RSA model are better than those of the KRG model, whereas the KRG model predicts equally well at the off‐Pareto‐region (region away from the Pareto‐optimal solutions), which is not the case with the RSA model. The local resampling of the Pareto‐optimal front increases the fidelity of the approximate solutions near the Pareto‐optimal region. The ratios of the channel height to the dimple print diameter and of the dimple print diameter to the dimple pitch are found to be more sensitive along the Pareto‐optimal front than the ratio of the dimple depth to the print diameter. The decrease of the ratio of the channel height to the dimple diameter and the increase of the ratio of the dimple print diameter to the pitch lead to greater heat transfer at the expense of the pressure loss, whereas the ratio of the dimple depth to the print diameter is rather insensitive to Pareto‐optimal solutions. Pareto‐optimal solutions at higher values of the Nusselt number are associated with higher values of the pressure loss due to the increased recirculation, mixing of fluid and vorticity generation. Copyright © 2010 John Wiley & Sons, Ltd.     

Effect of graded triple delta-doped sheets on the performance of GaAs based dual channel pseudomorphic high electron mobility transistors

The characteristics of InGaP/InGaAs/GaAs dual channel pseudomorphic high electron mobility transistors (DCPHEMTs) with different graded triple delta-doped sheets are investigated and experimentally demonstrated. Based on a two-dimensional simulator of ATLAS, the band diagrams, electron densities and DC characteristics of studied devices are comprehensively analyzed. Due to the use of properly graded triple delta-doped sheets, good pinch-off and saturation characteristics, improved transport properties and wide current swing are obtained. For comparison, a practical DCPHEMT with good device performances is fabricated as well. It is found that the simulated data are in good agreement with experimental results.     

Synthesis of poly(isopropenylphenoxy propylene carbonate) and its facile side‐chain functionalization into hydroxy‐polyurethanes

4‐Isopropenyl phenol ( 4‐IPP ) is a versatile dual functional intermediate that can be prepared readily from bisphenol‐A ( BPA ). Through etherification with epichlorohydrin to the phenolic group of 4‐IPP , it can be converted into 4‐isopropenyl phenyl glycidyl ether ( IPGE ). On further reaction with carbon dioxide in the presence of tetra‐n‐butyl ammonium bromide ( TBAB ) as the catalyst, IPGE was transformed into 4‐isopropenylphenoxy propylene carbonate ( IPPC ) in 90% yield. Cationic polymerization of IPPC with strong acid such as trifluoromethanesulfonic acid or boron trifluoride diethyl etherate as the catalyst at ?40 °C gave a linear poly(isopropenylphenoxy propylene carbonate), poly( IPPC ), with multicyclic carbonate groups substituted uniformly at the side‐chains of the polymer. The cyclic carbonate groups of poly( IPPC ) were further reacted with different aliphatic amines and diamines resulting in formation of polymers with hydroxy‐polyurethane on side‐chains. Syntheses, characterizations of poly( IPPC ) and its conversion into hydroxy‐polyurethane crosslinked polymers were presented. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 802–808     

A novel quasi-phase-matching frequency doubling technique

A new quasi-phase-matching technique for efficient second-harmonic generation is reported. It is based on the spatial periodic modulation of the light intensity along the propagation direction, rather than the conventional spatial periodic modulation of the nonlinear optical coefficients. It can be realized by using a novel dual-channel waveguide frequency doubler structure for the desired light intensity distribution. This dual-channel waveguide device has major advantages including very small beam size, high light intensity within long nonlinear-waveguide interaction length, highly efficient second-harmonic generation, ease in fabrication of the nonlinear channel waveguides without any spatially periodic poling, and low waveguide propagation losses. The new quasi-phase-matching technique can also be applied to third-harmonic generation and other nonlinear optics processes.     

The parameterization and validation of generalized born models using the pairwise descreening approximation

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.     

Performance of run-length limited (4, 18) code for optical storage systems

In this paper, the authors investigate the performance of recently presented run-length limited (4, 18) code for high density optical storage systems. The construction of the code is described simply. The code has code rate R = 1/3 and density ratio (DR) = 1.67. The bit error rate (BER) performance for decision feedback equalizer (DFE) and partial response maximum likelihood (PRML) detector are simulated, considering signal-to-noise ratio (SNR) and optical channel jitter. The result shows that the performance of the code is acceptable. The encoder and decoder of the code are implemented by complex programmable logic device (CPLD) chip and the hardware resources required for encoder and decoder arelow.