CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

单矢量水听器估计目标方位的方法与实验

为评估基于单矢量水听器的方位估计能力,在黄海海域对矢量水听器进行实验。矢量水听器吊放于接收船尾部,采用平均声强器和复声强器方位估计方法,并提出以概率密度值最大的方位角作为目标方位估计值的具体处理准则,对恒定方向、匀速行驶的目标船方位进行估计,并求出两种方法的方位估计误差。结果表明,水听器布放深度10 m时,对正横距离为0.42 km的航速10 kn的目标船,平均声强器方法的水平方位角估计误差18°,极角估计误差为5°,可以在离目标船最远1.17 km处估计其方位;复声强法的水平方位角估计误差为13°,极角估计误差为8°,可以在离目标船最远2.35 km处估计其方位。在有接收船的噪声干扰情况下,复声强器比平均声强器方法估计的方位更准确,可以对更远处的噪声源进行方位估计。     

Additive hazards regression with random effects for clustered failure times

Additive hazards model with random effects is proposed for modelling the correlated failure time data when focus is on comparing the failure times within clusters and on estimating the correlation between failure times from the same cluster, as well as the marginal regression parameters. Our model features that, when marginalized over the random effect variable, it still enjoys the structure of the additive hazards model. We develop the estimating equations for inferring the regression parameters. The proposed estimators are shown to be consistent and asymptotically normal under appropriate regularity conditions. Furthermore, the estimator of the baseline hazards function is proposed and its asymptotic properties are also established. We propose a class of diagnostic methods to assess the overall fitting adequacy of the additive hazards model with random effects. We conduct simulation studies to evaluate the finite sample behaviors of the proposed estimators in various scenarios. Analysis of the Diabetic Retinopathy Study is provided as an illustration for the proposed method.     

RP-HPLC-DAD method for the determination of phenylepherine,paracetamol, caffeine and chlorpheniramine in bulk and marketed formulation

A simple, specific and accurate isocratic RP-HPLC-DAD method was developed for the simultaneous determination of phenylephrine, paracetamol, caffeine and chlorpheniramine in bulk and tablet dosage form. The four contents are present in variable concentrations and have variable chromatographic behavior making the process of analysis very difficult. For present studies a reversed-phase C-18 column (150 mm × 4.5 mm i.d., particle size 5 μm) with mobile phase consisting of acetonitrile, methanol and 10 Mm phosphate buffer 16:22:62 (v/v) (pH of buffer 2.5 ± 0.02, adjusted with ortho phosphoric acid) was used. The flow rate was 1.0 ml/min and eluents were monitored at 280 nm. The mean retention times of phenylephrine, paracetamol, caffeine and chlorpheniramine were found to be 1.8, 3.1, 5.2 and 10.9 min, respectively. The method was validated in terms of linearity, range, specificity, accuracy, precision and robustness. The proposed method was successfully applied to the estimation of phenylephrine, paracetamol, caffeine and chlorpheniramine in combined tablet dosage form.     

融合STREAM理念的中学化学核心素养的培养及实践研究*——以“水的组成”为例

STREAM教育属于典型的跨学科教育形式,在学科融合的背景下,基于STREAM理念视角解决实际问题,注重在实践过程中培养和增强学生的批判思维与解决问题的能力,提升跨学科和创造性思维,使学生成为具有科学创新和革新精神的全面发展的人。融合STREAM理念开发初中化学教学案例,并将其应用于教学中,通过使用原创教学案例“水的组成”进行实践教学,研究其对教学效果及学生化学核心素养的提升作用;在实践过程中设有实验班与对照班,通过纸笔测试和问卷调查进行数据收集,结果显示不管在知识掌握度还是素养养成和促进方面,实验组都明显优于对照组,这说明融合STREAM理念对化学的教与学都具有积极作用。     

过渡态理论在化学体系中的2个应用实例*

在大学本科一二年级的物理化学教学中,化学动力学章节的学习涉及到对不同时间尺度的认识。本文利用过渡态理论得到的速率常数表达公式,以乙烷分子碳/碳单键旋转和水分子氢键交换的动力学过程为例,对这2个应用实例的动力学过程所发生的时间尺度做出估算。这些时间尺度的估算对于学生理解不同动力学过程的物理图像至关重要,同时也有助于加强学生对重要公式的理解并能够将这些公式在化学体系中灵活运用。     

Fabrication and Characterization of Zinc Oxide Nanowire Based Two-electrode Capacitive Biosensors on Flexible Substrates for Estimating Glucose Content in a Sample

The present work deals with fabrication and characterization of the zinc oxide (ZnO) nanowire based novel two-electrode capacitive biosensors on flexible Polyethylene terephthalate (PET) substrates for accurate estimation of glucose by analyzing the fundamental dielectric nature of the relevant sample. The morphology and crystalline quality of grown nanowires are analyzed by using field-emission scanning electron microscope (FESEM) and X-ray diffractometer (XRD), respectively. Current and capacitance values of the device have been studied for ten different glucose concentrations relevant to the physiological standards. The analytical performance of the devices in terms of enzyme activity, reliability and flexibility has also been evaluated.     

ECM and SAGE based joint estimation of timing and frequency offset for DMIMO–OFDM system

Distributed multiple-input multiple-output (DMIMO) technology is a key enabler of coverage extension and enhancement of link reliability in wireless networks through distributed spatial diversity. DMIMO employs classic relay channels in between the source and the destination to opportunistically form a virtual antenna array (VAA) for emulating cooperative diversity. Use of multiple antennas at the relays further increases capacity and reliability of the relay–destination channel through multiplexing and diversity of MIMO antennas respectively. In such network, the signal received at the destination is characterized by multiple timing offsets (MTO) due to different propagation delay and multiple carrier frequency offsets (MCFO) due to independent oscillators of the relays. Hence, synchronization becomes a crucial issue in DMIMO in order to realize the distributed coherence. In this paper, we address joint estimation of MCFO and MTO in DMIMO orthogonal frequency division multiplexing (OFDM) with MIMO configuration at the relays for estimate-and-forward (EF) relaying protocol. Two iterative algorithms, based on expectation conditional maximization (ECM) and space alternating generalized expectation–maximization (SAGE) are proposed for joint estimation in presence of inter carrier interference (ICI). The robustness of both the estimators to ICI is evaluated by mathematical analysis and supported by extensive simulations. The performance of the proposed estimators is assessed in terms of mean square error (MSE) and bit error rate (BER). The theoretical Cramer–Rao lower bound (CRLB) of estimator error variance is also derived.     

Optimal estimation of the diffusion coefficient from non-averaged and averaged noisy magnitude data

The magnitude operation changes the signal distribution in MRI images from Gaussian to Rician. This introduces a bias that must be taken into account when estimating the apparent diffusion coefficient. Several estimators are known in the literature. In the present paper, two novel schemes are proposed. Both are based on simple least squares fitting of the measured signal, either to the median (MD) or to the maximum probability (MP) value of the Probability Density Function (PDF). Fitting to the mean (MN) or a high signal-to-noise ratio approximation to the mean (HS) is also possible. Special attention is paid to the case of averaged magnitude images. The PDF, which cannot be expressed in closed form, is analyzed numerically. A scheme for performing maximum likelihood (ML) estimation from averaged magnitude images is proposed. The performance of several estimators is evaluated by Monte Carlo (MC) simulations. We focus on typical clinical situations, where the number of acquisitions is limited. For non-averaged data the optimal choice is found to be MP or HS, whereas uncorrected schemes and the power image (PI) method should be avoided. For averaged data MD and ML perform equally well, whereas uncorrected schemes and HS are inadequate. MD provides easier implementation and higher computational efficiency than ML. Unbiased estimation of the diffusion coefficient allows high resolution diffusion tensor imaging (DTI) and may therefore help solving the problem of crossing fibers encountered in white matter tractography.