Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.     

Scaling in Electrical Conductivity Measurements and Rheological Measurements of Monarch 700 Dispersions Stabilized by Polymers

For making stable dispersions of graphitic carbon black (Monarch 700), the effectiveness of three dispersants/polymers (hypermer LP1, hypermer B246, and OLOA 11000) in xylene is investigated. Hypermer LP1 (polyhydroxystearic acid) is a homopolymer and hypermer B246 (PEG 30-dipolyhydroxystearate) is a polyhydroxystearic acid/polyethylene oxide/polyhydroxystearic acid ABA block copolymer, while OLOA 11000 (polyisobutylene succinimide) has a polar head group (polyamine) attached to a hydrocarbon chain (polyisobutylene). Well-dispersed graphitic carbon black dispersions were prepared using dispersants at optimum concentrations. Percolation threshold and rheological threshold were determined by analyzing the variations in electrical conductivity and elastic modulus with concentration of carbon black. Above threshold concentration, scaling law was applied to experimental data of rheology (dynamic measurements) and electrical conductivity measurements to evaluate quality of the system. Effectiveness of polymers was investigated on the basis of value of critical exponent (t and t′, respectively) in scaling power law. Hypermer LP1 was proved to be a poor dispersant for Monarch 700 dispersions while other two polymers were found to be effective stabilizers.     

Research on application of polynomial fitting technique in rotary kiln infrared temperature measurement system

Aiming at the linear temperature compensation algorithm’s disadvantage of temperature measurement error in rotary kiln infrared scanning temperature measurement process, this paper proposes a precise nonlinear cubic polynomial fitting temperature compensation algorithm. The proposed algorithm compensates the temperature values of scanning points on rotary kiln surface by following steps: Calculating temperature difference between the real temperature value of rotary kiln and temperature value measured by infrared scanning temperature measurement system; Fitting the temperature difference data with cubic polynomial; Using the obtained function to compensate temperature. Experimental result shows that compared with the usual linear temperature compensation algorithm, the accuracy of proposed algorithm has raised about 2.25 times when cubic polynomial is used.     

Incompatibility networks as models of scale-free small-world graphs

We make a mapping from Sierpinski fractals to a new class of networks, the incompatibility networks, which are scale-free, small-world, disassortative, and maximal planar graphs. Some relevant characteristics of the networks such as degree distribution, clustering coefficient, average path length, and degree correlations are computed analytically and found to be peculiarly rich. The method of network representation can be applied to some real-life systems making it possible to study the complexity of real networked systems within the framework of complex network theory.     

利用多项式拟合测量飞机油箱油量

飞机飞行中,测量剩余油量是关乎飞行安全的重要工作。以往采用的查表法存在存储数据量过大的问题,而插值法的计算又过于复杂,为此,提出了一种基于多项式数据拟合的油箱剩余油量测量方法,该方法通过存储多项式系数减少数据存储量,通过将多元插值计算改为多项式计算降低运算量。实验中,首先通过地面实验数据拟合获取多项式参数,再利用飞机飞行中获取的测量数据进行计算,所得结果与油箱内剩余油量的实际测量结果相比较,测量误差满足使用要求。通过理论和实验分析,在多项式拟合的阶数选择上明确了使用三阶多项式的合理性。该方法有较好的实用性,已在实践中应用。     

非晶氮化铁薄膜的生长机制——传统动力学生长标度方法的适用性

采用动力学标度方法研究了磁控溅射沉积的非晶氮化铁薄膜的动力学生长机制, 结果表明, 具有连续类柱状岛形貌的非晶氮化铁薄膜具有标度不变的自仿射分形特点, 其粗糙度指数α=0.82±0.21, 生长指数β=0.44±0.07, 动力学标度指数1/z=0.54±0.07. 薄膜生长符合提出的热重新发射生长模型.     

非等熵气体动力学方程组大初值问题的放缩框架

非等熵气体动力学系统Cauchy问题弱解全局存在性有两个公开问题:一个是包含真空的小初值问题,另一个是任意大初值问题.本文通过引入一个放缩框架证明了上述两个问题的等价性,即对于粘性消失解,其包含真空小初值问题的一致BV估计蕴含着任意大初值问题弱解的全局存在性.该放缩框架对大多数具有物理背景的双曲守恒律系统亦成立.     

多项式偏最小二乘法对非线性体系红外谱图的分析

文章利用了一种非线性模型多项式偏最小二乘法(PPLS),结合傅里叶变换红外光谱遥感技术,对大气中的五组分混合体系进行了同时分析。并与偏最小二乘法(PLS)得到的结果进行了比较,PPLS显示出较好的处理非线性数据的能力。尤其是对混合物中的苯和氯仿的预测,均方根预测误差(RMSEP)分别是0.043和0.087,用PLS预测相应的RMSEP为0.402和0.842。PPLS的这一预测精度,可以满足遥感傅里叶变换红外光谱对大气中有毒气体的实时、在线监测的需要。同时PPLS可以用较少的潜变量对变量进行解释,显示出PPLS模型的稳健性和简单化。