A new class of conformable spectral observers for signal reconstruction

In this work, the design of spectral observers for signal reconstruction based on Kalman filters is performed and evaluated. The conformable derivative and the beta‐derivative were used to design the Kalman filters. Both derivatives satisfy the same formulas of the classical derivation, eg, the chain rule. The derivative order, the Ricatti equation parameters, and the observers tuning parameters were optimized using an optimization algorithm based on the bat's echolocation behavior (Bat algorithm). The simulation results showed the advantages of using the proposed observers for the signal reconstruction.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

统计数据采样算法

将集中式控制系统常用的结构二层结构改进为智能化的三层结构的设计方案,即传感器、智能巡检仪和上位机。上位机既可以直接读取传感器的数据也可读取智能巡检仪的数据。此方案较好地解决了二层结构所出现的问题,并且也适合交大规模的其它类型的控制系统。这种设计方案存在当规模时上位机采集数据出现丢失现象。本文提出了利用数据库的历史数据及控制曲线的线性特征的数据采集算法,较好地解决了数据丢失的问题。并以温控系统为例仿真了在较大规模控制环境下的试验结果。     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Combined Experimental and Theoretical Insights into the Corrosion Inhibition Activity on Carbon Steel Iron of Phosphonic Acids

The inhibition effect of N,N′-phosphonomethylglycine (PMG) and vinyl phosphonic acid (VPA) on the 3% NaCl acidic solution corrosion of carbon steel iron was studied at different immersion times by potentiodynamic polarization, electrochemical impedance spectroscopy, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, and computational methods. It is found from the polarization studies that PMG and VPA behave as mixed-type inhibitors in NaCl. Values of charge transfer resistance (R_ct) and double layer capacitance (C_dl) in the absence and presence of inhibitors are determined. The PMG and VPA inhibitors were capable of inhibiting the corrosion process up to ≈91% and ≈85%, respectively. In the presence of PMG, the synergic effect of chlorine ions was observed. Density functional theory (DFT) was engaged to establish the adsorption site of PMG, VPA, and their deprotonated states. For studied compounds, the resulted values of E_LUMO, E_HOMO, energy gap (∆E), dipole moment (μ), electronic hardness (η), global softness (σ), electrophilic index (ω), and the electronic potential map are in concordance with the experimental data results regarding their corrosion inhibition behavior and adsorption on the metal surface.     

Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free-energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.     

基于柔性碳纳米管压阻膜的无线加速度检测系统

通过对加速度检测的重大意义进行分析,得出了加速度检测仪的价值和意义,介绍了本系统的设计思路和应用前景。传感器采用了基于纳米技术的碳纳米管薄膜感应前端,拓宽了传感器设备的研发领域,同时应用无线传感技术,使系统进一步实用化。最后介绍了本系统的实验情况,以及具体应用的效果。     

Automatic analysis of microscopic photo-pictures of undeveloped and developed nuclear emulsions

Methods of automatic computer analyses of images have large impotence in numerous physical problems with different kinds of radiations, which use such solid-state detectors as nuclear photographic emulsions, plastics and others. We described a method of expanding boundaries of dark areas for such computer analyses of micro-pictures. We demonstrated effectiveness of this method by the example of the search of microcrystals size distributions in two undeveloped nuclear emulsions and similar distribution of background grains in the developed emulsion.     

Formation of longitudinal aggregation of inclusions in bulk sapphire and yttrium‐aluminum garnet grown by horizontal directed crystallization method

It is shown that the formation of longitudinal aggregation of inclusions in bulk sapphire and yttrium‐aluminum garnet (YAG) grown by the method of HDC is caused by local accumulation of impurities, disturbance of morphological stability of the crystallization front and capture of inclusions and impurities in the nodal region of the melt two‐vortex convection. Studied is the influence of thermal and geometrical parameters of the melt and the shape of the crystallization front on the conditions of the formation of the capture of inclusions.