Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes

Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

Short-surface waves radiated by a partially-immersed 3-dimensional oscillating body

The short-surface waves generated by a 3-D arbitrarily oscillating body floating onwater are discussed. In the far-field off the body, the phase and the amplitude functions ofthe radiated waves are determined by the ray method. An undetermined constant is includ-ed in the amplitude function. From the result of Ref. [1], the near-field boundary layersolution near the body waterline is obtained. The amplitude of this solution depends on thewhole wall shape of the body and the slope at the body waterline on the cross-sections per-pendicular to the waterline. By matching the far-field solution with the near-field bound-ary layer solution, the undetermined constant in the amplitude function of the far-fieldradiated waves is determined. For the special case of a half-submerged sphere which per-forms vertical oscillating motion, the result obtained in this paper is in agreement withthat of Ref. [ 2 ].

Multiscale Method for Turbulent-Flow Computations

A main method of predicting turbulent flows is to solve LES equations, which was called traditional LES method. The traditional LES method solves the motions of large eddies of size larger than filtering scale An while modeling unresolved scales less than Delta_n. Hughes et al argued that many shortcomings of the traditional LES approaches were associated with their inabilities to successfully differentiate between large and small scales. One may guess that a priori scale-separation would be better, because it can predict scale-interaction well compared with posteriori scale-separation. To this end, a multi-scale method was suggested to perform scale-separation computation. The primary contents of the multiscale method are l) A space average is used to differentiate scale. 2) The basic equations include the large scale equations and fluctuation equations. 3) The large-scale equations and fluctuation equations are coupled through turbulent stress terms. We use the multiscale equations of n=2, i.e., the large and small scale (LSS) equations, to simulate 3-D evolutions of a channel flow and a planar mixing layer flow Some interesting results are given.

Quantifying Earthquake Collapse Risk of Tall Steel Braced Frame Buildings Using Rupture-to-Rafters Simulations

This thesis examines collapse risk of tall steel braced frame buildings using rupture-to-rafters simulations due to suite of San Andreas earthquakes. Two key advancements in this work are the development of (i) a rational methodology for assigning scenario earthquake probabilities and (ii) an artificial correction-free approach to broadband ground motion simulation. The work can be divided into the following sections: earthquake source modeling, earthquake probability calculations, ground motion simulations, building response, and performance analysis.

As a first step the kinematic source inversions of past earthquakes in the magnitude range of 6-8 are used to simulate 60 scenario earthquakes on the San Andreas fault. For each scenario earthquake a 30-year occurrence probability is calculated and we present a rational method to redistribute the forecast earthquake probabilities from UCERF to the simulated scenario earthquake. We illustrate the inner workings of the method through an example involving earthquakes on the San Andreas fault in southern California.

Next, three-component broadband ground motion histories are computed at 636 sites in the greater Los Angeles metropolitan area by superposing short-period (0.2~s-2.0~s) empirical Green's function synthetics on top of long-period ($>$ 2.0~s) spectral element synthetics. We superimpose these seismograms on low-frequency seismograms, computed from kinematic source models using the spectral element method, to produce broadband seismograms.

Using the ground motions at 636 sites for the 60 scenario earthquakes, 3-D nonlinear analysis of several variants of an 18-story steel braced frame building, designed for three soil types using the 1994 and 1997 Uniform Building Code provisions and subjected to these ground motions, are conducted. Model performance is classified into one of five performance levels: Immediate Occupancy, Life Safety, Collapse Prevention, Red-Tagged, and Model Collapse. The results are combined with the 30-year probability of occurrence of the San Andreas scenario earthquakes using the PEER performance based earthquake engineering framework to determine the probability of exceedance of these limit states over the next 30 years.

A novel MPT noise prediction methodology for highly-integrated propulsion systems with inlet flow distortion

Embedded propulsion systems, such as for example used in advanced hybrid-wing body aircraft, can potentially offer major fuel burn and noise reduction benefits but introduce challenges in the aerodynamic and acoustic integration of the high-bypass ratio fan system. A novel approach is proposed to quantify the effects of non-uniform flow on the generation and propagation of multiple pure tone noise (MPTs). The new method is validated on a conventional inlet geometry first. The ultimate goal is to conduct a parametric study of S-duct inlets in order to quantify the effects of inlet design parameters on the acoustic signature. The key challenge is that the mechanism underlying the distortion transfer, noise source generation and propagation through the non-uniform flow field are inherently coupled such that a simultaneous computation of the aerodynamics and acoustics is required. The technical approach is based on a body force description of the fan blade row that is able to capture the distortion transfer and the MPT noise generation mechanisms while greatly reducing computational cost. A single, 3-D full-wheel unsteady CFD simulation, in which the Euler equations are solved to second-order spatial and temporal accuracy, simultaneously computes the MPT noise generation and its propagation in distorted mean flow. Several numerical tools were developed to enable the implementation of this new approach. Parametric studies were conducted to determine appropriate grid and time step sizes for the propagation of acoustic waves. The Ffowcs-Williams and Hawkings integral method is used to propagate the noise to far field receivers. Non-reflecting boundary conditions are implemented through the use of acoustic buffer zones. The body force modeling approach is validated and proof-of-concept studies demonstrate the generation of disturbances at both blade-passing and shaft-order frequencies using the perturbed body force method. The full methodology is currently being validated using NASA's Source Diagnostic Test (SDT) fan and inlet geometry. Copyright © 2009 by Jeff Defoe, Alex Narkaj & Zoltan Spakovszky.

Design and path planning for a remote-brained service robot

This article introduced an effective design method of robot called remote-brain, which is made the brain and body separated. It leaves the brain in the mother environment, by which we mean the environment in which the brain's software is developed, and talks with its body by wireless links. It also presents a real robot TUT06-B based on this method which has human-machine interaction, vision systems, manipulator etc. Then it discussed the path planning method for the robot based on ant colony algorithm in details, especially the Ant-cycle model. And it also analyzed the parameter of the algorithm which can affect the convergence. Finally, it gives the program flow chat of this algorithm.

立构规整型聚(3-烷基噻吩)的结晶形态与结构研究

立构规整聚(3-烷基噻吩)是具有高功能的聚合物光电材料，被广泛用于有机光电器件的制备与集成。本论文利用一种新的结晶方法，即溶剂辅助结晶，得到了梳状刚性链高分子RR-P3BT毫米级的新晶体及其晶胞参数。同时，还得到了RR-P3BT的分子链在这种新晶体中的堆砌方式。首次直接证明了刚性链高分子RR-P3BT的晶体生长方式是层状生长。又采用溶液等温结晶的方法，得到了RR-P3BT的多种晶体。包括Whisker晶体，平行四边形片晶，小长方形片晶和棒状单晶。并得出了这些晶体的晶胞参数和分子链的堆砌方式。通过溶液等温结晶也得到了RR-P3HT的多种晶体。包括Whisker晶体，长方形片晶，平行四边形片晶和六边形片晶。并得出这些晶体的晶胞参数和分子链的堆砌方式。

人类带3蛋白胞质片段的表达纯化及其性质表征

带3蛋白胞质片段(cdb3)具有多种生理功能：它可以将膜和膜骨架蛋白相联，起着维持细胞形状以及沟通内外环境的作用。而且，它还通过与多个糖酵解酶的相互作用来调节红细胞内糖酵解速率。它的这些功能很大程度上归因于它的分子柔性大，可以通过各种构象与膜蛋白、糖酵解酶等竞争性结合。 在本文中，我们首先运用分子克隆技术在大肠杆菌BL21(DE3)中成功地构建pET28b-cdb3表达体系。经37℃培养至OD600达0.6时，加入1mM IPTG ，于30℃诱导表达cdb3蛋白。经离子交换和亲和层析两步纯化得到电泳纯的具有生物活性的cdb3蛋白。之后，我们首次较为系统地表征了cdb3蛋白的构象特点：在常规的生理环境下, cdb3蛋白呈现典型的α-螺旋、β折叠二级结构， cdb3的四个Trp残基很大程度地包埋于疏水环境中；随溶液GuHCl浓度增加，cdb3 的四个Trp残基逐渐暴露于极性环境中；当pH值从6.0升高到10.0时，cdb3的Tm值逐渐降低约15℃，其内源荧光强度增加两倍，并在pH 7.2和pH9.2处呈现拐点，而蛋白的二级结构却没有发生变化。金属离子Cd2+、Ca2+、Cu2+、Co2+、Mg2 、Zn2+的结合位点在cdb3蛋白的Trp残基附近，而50μM的金属离子对重组cdb3蛋白的二级结构影响微小。最后，我们合成了cdb3蛋白N端肽段1－23，发现其在水溶液中呈无规卷曲结构，TFE可诱导其形成α螺旋，当TFE浓度增至80%时α螺旋含量达最高。无规卷曲的肽段不与醛缩酶相结合，其以α螺旋形式与醛缩酶相结合。 ATP可与肽段、重组cdb3蛋白结合，并对其光谱学性质有一定影响。当ATP浓度达到3mM时，重组cdb3蛋白发生聚集。

铬系催化剂聚合1,3-双烯烃的研究

铬系催化剂是合成1,2-聚丁二烯和3,4-聚异戊二烯的一种主要催化剂体系，1,2-聚丁二烯和3,4-聚异戊二烯是制造高性能轮胎的重要原料。本论文研究了以含氮化合物和含磷化合物为配体的铬催化剂合成1,2-聚丁二烯和3,4-聚异戊二烯的反应规律。 1. 以邻菲咯啉为配体的铬催化剂在己烷中50℃下可获得1,2-结构、顺-1,4-结构和反-1,4-结构单元含量分别约为50%、30%和20%，分子量呈双峰分布的聚丁二烯。改变聚合温度，可有效控制聚合物的1,2-结构含量和分子量及分布。催化剂通过预陈化方式，可有效抑制低聚物的生成。 2. 以亚磷酸二烷基酯为配体的铬催化剂是合成1,2-聚丁二烯的高效催化剂，所得聚合物具有高的1,2-结构含量（> 78%）。改变烷基铝和亚磷酸二烷基酯的结构，可以得到高熔点或低熔点间同1,2-聚丁二烯和无规1,2-聚丁二烯。催化剂以现配方式的活性最高。 3. 以磷酸三苯酯为配体的铬催化剂可获得间同1,2-聚丁二烯，而聚合物中含有低聚物。催化剂以现配方式的活性最高。聚合物的熔点，低聚物的含量与磷酸三苯酯的结构有一定的关系。 4. 以邻菲咯啉为配体的铬催化剂在50℃下聚合异戊二烯，具有高的催化活性，可获得3,4-结构含量约67%的高分子量无规3,4-聚异戊二烯。催化剂的组成对聚合物的微观结构无明显影响。改变聚合温度，可有效控制聚合物的3,4-结构含量和分子量及分布。

中空纤维膜基萃取稀土的研究：中空纤维膜基萃取Ce~(4+), Th~(4+)和RE~(3+)及其传质动力学

本文用中空纤维膜基萃取法研究了铈（IV）、钍和 RE（III）的膜基萃取；铈（IV）与 RE（III）、钍和 RE（III）的膜基萃取分离；铈（IV）与 RE（III）的界面化学反应动力学；膜基萃取中的流体动力学；萃取操作中乳化发生的机理；测定了中空纤维膜的孔率和孔径。在铈（IV）、钍和 RE（III）的膜基萃取过程中，研究了水相流量、油相流量、原料液中硫酸浓度、萃取剂 N1923浓度和水相溶质浓度对基于水相总传质系数的影响。钍的总传质系数受水相流量影响较大，不受油相流量影响，从而提出水相扩散层控制的膜基萃取传质机理；铈（IV）的传质系数受水相流量影响，油相流量影响较小，主要为水相扩散层控制的传质机理；RE（III）的传质系数受水相和油相的影响都比较小，为膜内传质过程的传质机理。酸浓度对钍和铈（IV）传质系数影响较小，是由于酸浓度影响分配系数，而对于水相扩散控制的传质过程，水相分传质系数与分配系数无关；酸浓度对 RE（III）的影响，是由于膜内传质阻力与分配系数在关；N1923 对 RE（III）萃取传质系数的影响进一步证明膜内过程控制的传质机理，同时对数曲线的斜率大于1 也说明界面反应为一复杂过程；水相溶质浓度不影响基于水相的总传质系数，进一步证实了传质速度与初始浓度无关，也从一个侧面反应了膜基萃取实验有较好的重复性。实验研究的结果，对铈（IV）的膜基萃取选择油相组成为 10%N1923+4%异辛醇+正庚烷（或煤油），水相酸浓度为 1～2mol/L，水相和油相流量可以在较大的范围内选择；钍的膜基萃取条件相似，只是油组成中萃取剂浓度为 1%N1923。在流体动力学部分，通过作用力分析，利用能量守恒原理，推导出了膜基萃取操作中的雷诺数，建立了层流流动模型；腔内外流体流速的径向分布模型和平均流速的计算式；腔内外压力沿管长度分布的数学模型，并得到了两相流体的压力差计算式。流体的动力学分析对于研究乳化发生的机理、传质的数学模型和扩散层厚度等皆有理论价值。通过流体动力学理论，结合膜破裂压和界面张力的实验方法研究了乳化发生的机理。水相进入有机相的乳化，对于非同级萃取，外压作用是乳化的主要原因，提出了类似于重力液滴形成的乳化模型；对于有机相进入水相的乳化，亲油膜的表面易形成油膜及界面张力形成的附加压力是乳化的基本原因，而随着有机相内溶质浓度增加界面张力降低使乳化在萃取操作的后期较易发生。膜破裂压和界面张力的研究方法使乳化的研究变得可以进行实验测定，这对于膜材的选择是很有价值的。界面反应动力学采用了上升单滴法，这种方法一般具有实验重复性较差的缺点。通过实验发现，影响重复性的因素主要是单滴形成速率的稳定性、聚结界面处油水界面位置的恒定和扩散传质的消除等。我们采用盘管式油加液管的设计，比较简单地解决了单滴形成速率稳定的问题，油水界面恒定是一个技术性问题，在实验中得到了较好的解决，通过传质时间与控制聚结界面的面积解决了消除扩散传质的难题。本论文的创新之处有如下几个方面：1．根据氟碳铈矿中钍、铈（IV）与稀土（III）分离的总目标，首次实现了伯胺 N1923对上述离子的中空纤维膜基萃取，提出了利用动力学差异的新型分离模式；2．对流量改变对传质系数的影响，所有文献报道的流量范围都没有达到流量增加使传质系数减小，而这一较高的流量揭示了油水界面随压力增加向膜内移动的事实，这对防止乳化时的压力控制是非常重要的。流量对扩散层厚度影响是对传质系数影响的主要原因，而混流的影响是次要的因素；3．铈（IV）和 RE（III）、钍和 RE（III）的分离表明，分离系数远远大于由总传质系数预计的结果，从而提出了动力学竞争萃取分离的机理；4．膜破裂压的测定方法是一个创新的设计。这种方法对于膜材选择和萃取时操作压力的控制是非常重要的。在现有文献中，都是直接在膜萃取操作时测定水相中的游离油或油相中游离水的体积的方法进行研究，这即不能研究乳化的机理，也不能测定准确的乳化时间。因此膜破裂压测定为乳化过程提供了一个新的研究方法；5．乳化机理的研究得到了较新的结论，尤其对于油相进入水相的乳化机理，较好地解释了在水相有超压存在下油相漏液的原因；6．界面反应动力学实验装置中盘管式油相加样解决了油滴形成稳定性的问题，提高了实验测定的可靠性的重复性。

ABF＿3型复合氟化物的无机合成及稀土掺杂特性研究

本文介绍了钙钛矿型复合氟化物的基本知识和研究进展，并在已有文献的基础上对部分ABF＿3型氟化物的无机合成作了深入研究，进一步讨论了该类化合物的稀土掺杂特性和能量传递现象。首次以条件温和的中温水热法合成了重要激光基质材料KZnF_3、NaZnF_3。产物结构经XRD、SEM、XPS表征，IR和热分析证实水热产物未明显含有分子内结晶水。摸索了最佳合成条件，并比较了与固相合成产物在含氧量上的差异。水热法还实现了Eu的掺杂，荧光光谱和ESR谱均确认Eu进入格位并部分发生价态转变，讨论了Eu~(2+)格位取代和电荷补偿等问题。固相反应合了BaLiF_3:Eu:Gd磷光体多晶粉末。荧光光谱确认体系中Gd~(3+) → Eu~(2+)能量传递的存在。以DEXTER能量传递理论为基础，建立了能量传递模型，计算了能量传递几率，观察到Gd~(3+)和Eu~(2+)之间存在竞争吸收，当Gd~(3+)离子浓度过高，Eu~(2+)发射强度降低。

稀土对红细胞及带3蛋白胞质片段结构和生理功能的影响

稀土在农业和医学中的广泛应用使人们日益关心稀土的安全性问题。本论文以红细胞为研究对象，围绕稀土对红细胞形态的影响，稀土能否进入红细胞以及稀土对红细胞带3蛋白胞质片段结构和功能的影响三方面开展研究工作，主要研究成果如下：首先，在宏观上通过超高倍光学显微镜观察了稀土阳离子及其络阴离子对正常人红细胞形态的影响。结果表明当红细胞与硝酸悯作用后其体积发生膨胀，表面出现棘状凸起，细胞间发生聚集。而以往被人们认为毒性较小的柠檬酸悯则使红细胞呈现囊泡状凸起，随着与稀土作用时间的延长多数囊泡状结构可脱落。EDTA的加入可使部分在低浓度（10~(-7)M）稀土离子条件下变形的红细胞恢复原状，说明细胞形态变化主要是由环境中稀土的存在引起的。其次，根据稀土离子跨膜研究中存在的一些问题，在总结前人工作的基础上，建立一种方法测定了体外温育和静脉注射条件下红细胞中稀土含量。进一步证实文献报道含有络合剂的洗涤缓冲液能够将进入细胞内部的稀土带出，影响测定结果的准确性。本论文中应用不含络合剂的洗涤缓冲液洗涤与稀土温育后的红细胞，在10mMTris-HCl印H7.0）低渗缓冲液中溶胀，ICP-MS测定结果显示无论是稀土阳离子还是稀土络阴离子均可以跨膜，且稀土络阴离子跨膜速度较快。耳静脉注射稀土后仅在兔血浆及红细胞膜上检测到稀土，说明在短期静脉注射条件下存在于血浆中的稀土不能进入兔红细胞。最后，应用基因工程技术克隆、表达、纯化了带3蛋白胞质片段及其融合蛋白。计算机结构模拟、荧光光谱以及生物活性的测定证实重组带3蛋白胞质片段与天然蛋白具有相似的空间结构和生物活性。稀土离子对醛缩酶、醛缩酶与带3蛋白胞质片段相互作用的影响表现为：0-10μMLa~(3+) 对醛缩酶活性有促进作用，当体系中L~(3+)浓度达到6μM时，带3蛋白胞质片段基本完全失去对醛缩酶活性的抑制作用。蛋白质内源荧光和同步荧光光谱研究结果表明，La~(3+)对带3蛋白胞质片段与醛缩酶结构均具有一定影响。本论文实验结果表明，低浓度稀土可导致调节细胞内糖酵解速率的带3蛋白胞质片段失去活性，使糖酵解速率无序增强。由于红细胞主要碳源来自于血糖，糖酵解速率的加快很可能会引起生物体血糖浓度的降低。

聚3—羟基丁酸酯与聚丙撑碳酸酯共混体系研究

本论文对完全生物降解聚（3—羟基丁酸酯）（PHB）和聚丙撑碳酸酯（PPC）共混体系进行了全面研究，目的是提高PHB的综合性能，加深对共混高聚物的基本物理问题的认识，进一步明晰高聚物的结构和性能之间的关系.1.在分析判断PPC的热降解机理的基础上，对PPC进行了封端处理，阻止了以端羟基回咬“解拉链”方式引起的热降解，增加了PPC热降解反应活化能，显著地提高了PPC的稳定性（提高30K以上）.2.经热性能和形态结构等方面的表征，PHB/PPC共混体系为不相容体系，直接在PHB中加入PPC不能改善PHB的韧性和其它力学性能.3.PCL-PEG-PCL嵌段共聚物能够作为PHB/PPC的增容剂，在PHB/PPC共混体系中加入PCL-PEG-PCL三嵌段共聚物能显著减小分散相的平均尺寸.4.选用增塑剂对PPC进行增塑能够在很大范围内（80K）调节PPC的玻璃化转变温度，使PPC表现出弹性体的特性，拓宽了PPC的应用范围.5.增塑剂1,2丙二醇碳酸酯（PGC）对PHB有一定的增塑作用，但不能明显改善PHB的力学性能.6.增塑后的PPC是PHB的良好增韧剂，使PHB由脆性断裂转变为韧性断裂，最佳增韧效果可使PHB的抗冲击强度由36J/m增加到70PHB/30PPC/20PGC的307J/m，增加8倍.7.增塑后的PPC能够实现对PHB增韧，是增塑剂使得PPC在冲击实验条件下仍然保持弹性体的性质，由此引发空洞化、多重银纹和剪切屈服共存的增韧方式提高PHB的性能.

聚（3-羟基烷酸酯）的改性研究

该论文目的是改性细菌合成的聚(3-羟基丁酸酯)(PHB)及其共聚物(PHBV),采用交联或共混的方法,改变其聚集态结构或超分子结构,从而改善其力学性能.加深对高聚物结构与性能之间关系,高聚物结晶规律、及特殊相互作用在高聚物中作用的认识.1.采用反应性加工,用过氧化二异丙苯(DCP)引发PHBV的自由基链转移反应,产生了支化和交联的化学结构.2.用交联助剂二苯甲撑双马来酰亚胺(BMI)实现了PHBV的γ-辐射交联.交联的PHBV熔点和结晶度下降.3.双酚A(BPA)在PHBV/BPA共混物中起到了物理交联剂的作用.4.氢键交联结构使PHBV的链段运动受限,结晶速率下降.5.对叔丁基苯酚(TBP)在PHBV中形成了氢键接枝的超分子结构.6.经过溶液共混,BPA在PHB中起到了物理交联剂的作用,使PHB的断裂伸长率从3%提高到45%.8.二醋酸纤维素(CDA)与PHBV经溶液共混(混合溶剂氯仿/丙酮),PHBV的力学性能没有改善,原因可能是CDA-PHBV分子间的氢键作用较弱,组分间发生严重相分离,不利于性能提高.