Closed Loop Predictive Optimal Control Algorithm Using ARMA Models

A predictive optimal control algorithm based on auto-regressive moving average (ARMA) models has been developed. Being a closed loop algorithm, it can be used in the control of structures against any source of random excitation without any special arrangement for measuring the excitation. The algorithm combines two mathematical models: (1) An ARMA model representing the environment and the structure as a single system subjected to the unknown random excitation; and (2) a single-degree-of-freedom system, which represents the structure subjected to a known history of control force only. Unlike some ARMA based control algorithms, which are only for seismic excitations, the proposed algorithm permits the control system to be operational under any type of dynamic load. This results in a large reduction in the standby time of the control system and increases its reliability. In comparison with these algorithms, the proposed algorithm requires less measurements and sensors. The algorithm has the option for reducing or avoiding time delay.     

Structure/Control Synthesis with Nonnegligible Actuator Mass

Simultaneous design of a structure/active control system in which the mass of the actuators required to implement the active control is considered is addressed. The inclusion of required actuator mass essentially tightens the coupling between structure and control dynamics and introduces an inner iteration loop in the overall design process. Because this inner iteration loop significantly increases the computational burden, an algorithm for estimating the required actuator mass, given the control law and the desired maneuver, is presented. Additionally, a secant‐based actuator mass update algorithm is investigated in order to improve convergence characteristics of the inner iteration loop. A nonlinear optimization algorithm is used to direct the design process. The methodology is demonstrated on the design of a large two‐dimensional L‐shaped structure in which it is desired to minimize the line‐of‐sight‐pointing error between the two ends of the L after a worst‐case slew maneuver.     

集总干扰下六旋翼飞行器的轨迹跟踪控制

针对复杂集总干扰下六旋翼飞行器轨迹跟踪控制问题,给出了混合积分反步法控制与线性自抗扰控制的控制算法. 首先,通过牛顿-欧拉方程建立六旋翼飞行器的非线性动力学模型,并剖析系统输入输出的数学关系. 其次,根据六旋翼飞行器动力学模型的特点,将其分为位置与姿态两个控制环. 位置环采用积分反步法控制理论设计控制器,通过引入积分项来提高系统的抗干扰能力,消除轨迹跟踪的静态误差;姿态环采用线性自抗扰控制技术设计控制器,通过线性扩张观测器估计和补偿集总干扰影响,提高系统的鲁棒性. 最后,通过2组仿真算例和1组飞行试验验证了本文所提飞行控制算法的有效性. 研究结果表明:该控制算法对集总干扰有较好的抑制作用,能够使六旋翼飞行器既快又稳地跟踪上参考轨迹,具有一定的工程应用价值.      

A genetic algorithm based molecular modeling technique for RNA stem-loop structures

A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position.     

Vibration Control of Wind-Excited Tall Buildings Using Sliding Mode Fuzzy Control

A sliding mode fuzzy control (SMFC) is proposed to design a controller for the third-generation benchmark problem on wind-excited buildings. A distinctive feature in vibration control of large civil infrastructure is the existence of large disturbances, such as wind, earthquake, and sea wave forces. Those disturbances govern the behavior of the structure; however, they cannot be precisely measured, especially for the case of wind excitations. Since the structural accelerations are measured only at a limited number of locations without the measurement of the wind forces, the structure of the conventional control may have the feedback loop only. The general structure of the SMFC, proposed herein, is composed of a compensation part and a convergent part. The compensation part prevents the system from diverging, and the convergent part directs the system to the sliding surface. The compensation part uses not only the structural response measurement but also the disturbance measurement, so the SMFC has a feedback loop and a feedforward loop. To realize the virtual feedforward loop for the wind-induced vibration control, a disturbance estimation filter is introduced. The structure of the filter is constructed based on an autoregressive model for the stochastic wind force. This filter estimates the wind force at each time instance based on the measured structural responses and the stochastic information of the wind force. For verification of the proposed algorithm, numerical simulation is carried out on the benchmark problem for wind-excited buildings. The results indicate that the present control algorithm is efficient for reducing the wind-induced vibration.     

Three-dimensional folding of an RNA hairpin required for packaging HIV-1

An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.     

Agonist-induced changes in substituted cysteine accessibility reveal dynamic extracellular structure of M3-M4 loop of glutamate receptor GluR6

Recent evidence suggests that the transmembrane topology of ionotropic glutamate receptors differs from other members of the ligand-gated ion channel superfamily. However, the structure of the segment linking membrane domains M3 and M4 (the M3-M4 loop) remains controversial. Although various data indicate that this loop is extracellular, other results suggest that serine residues in this segment are sites of phosphorylation and channel modulation by intracellular protein kinases. To reconcile these data, we hypothesized that the M3-M4 loop structure is dynamic and, more specifically, that the portion containing putative phosphorylation sites may be translocated across the membrane to the cytoplasmic side during agonist binding. To test this hypothesis, we mutated Ser 684, a putative cAMP-dependent protein kinase site in the kainate-type glutamate receptor GluR6, to Cys. Results of biochemical and electrophysiological experiments are consistent with Cys 684 being accessible, in the unliganded state, from the extracellular side to modification by a Cys-specific biotinylating reagent followed by streptavidin (SA). Interestingly, our data suggest that this residue becomes inaccessible to the extracellular biotinylating reagent during agonist binding. However, we find it unlikely that Cys 684 undergoes membrane translocation, because the addition of SA to Cys-biotinylated GluR6(S684C) has no effect on peak glutamate-evoked current and only a small effect on macroscopic desensitization. We conclude that residue 684 in GluR6 is extracellular in the receptor-channel's closed, unliganded state and does not cross the membrane after agonist binding. However, an agonist-induced conformational change in the receptor substantially alters accessibility of position 684 to the extracellular environment.     

High-resolution NMR study of a GdAGA tetranucleotide loop that is an improved substrate for ricin, a cytotoxic plant protein

Ricin is a cytotoxic plant protein that inactivates ribosomes by hydrolyzing the N-glycosidic bond at position A4324 in eukaryotic 28S rRNA. Recent studies showed that a four-nucleotide loop, GAGA, can function as a minimum substrate for ricin (the first adenosine corresponds to the site of depurination). We previously clarified the solution structure of this loop by NMR spectroscopy [Orita et al. (1993) Nucleic Acids Res. 21, 5670-5678]. To elucidate further details of the structural basis for recognition of its substrate by ricin, we studied the properties of a synthetic dodecanucleotide, r1C2U3C4A5G6dA7G8A9U10G11A12G (6dA12mer), which forms an RNA hairpin structure with a GdAGA loop and in which the site of depurination is changed from adenosine to 2'-deoxyadenosine. The N-glycosidase activity against the GdAGA loop of the A-chain of ricin was 26 times higher than that against the GAGA loop. NMR studies indicated that the overall structure of the GdAGA loop was similar to that of the GAGA loop with the exception of the sugar puckers of 6dA and 7G. Therefore, it appears that the 2'-hydroxyl group of adenosine at the depurination site (6A) does not participate in the recognition by ricin of the substrate. Since the 2'-hydroxyl group can potentially destabilize the developing positive charge of the putative transition state intermediate, an oxycarbonium ion, the electronic effect may explain, at least in part, the faster rate of depurination of the GdAGA loop compared to that of GAGA loop. We also show that the amino group of 7G is essential for substrate recognition the ricin A-chain.     

The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution

The structure of an RNA hairpin containing a seven-nucleotide loop that is present in the self-cleaving sequence of hepatitis delta virus antigenomic RNA was determined by high resolution NMR spectroscopy. The loop, which is composed of only one purine and six pyrimidines, has a suprisingly stable structure, mainly supported by sugar hydroxyl hydrogen bonds and base-base and base-phosphate stacking interactions. Compared with the structurally well-determined, seven-membered anticodon loop in tRNA, the sharp turn which affects the required 180 degrees change in direction of the sugar-phosphate backbone in the loop is shifted one nucleotide in the 3' direction. This change in direction can be characterized as a reversed U-turn. It is expected that the reversed U-turn may be found frequently in other molecules as well. There is evidence for a new non-Watson-Crick UC base pair formed between the first and the last residue in the loop, while most of the other bases in the loop are pointing outwards making them accessible to solvent. From chemical modification, mutational and photocrosslinking studies, a similar picture develops for the structure of the hairpin in the active ribozyme indicating that the loop structure in the isolated hairpin and in the ribozyme is very similar.     

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement

We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA "kissing" hairpin complex formed between the HIV-2 TAR hairpin loop and a hairpin with a complementary loop sequence. Kissing hairpins are important in natural antisense reactions; their complex is a specific target for protein binding. The complex has all six nucleotides of each loop paired to form a bent quasicontinuous helix of three coaxially stacked helices: two stems plus a loop-loop interaction helix. Experimental constraints derived from heteronuclear and homonuclear NMR data on 13C and 15N-labeled RNA led to a structure for the loop-loop helix with an average root-mean-square deviation of 0.83 (+/-0.10) A for 33 converged structures relative to the average structure. The loop-loop helix of the kissing complex is distorted compared to A-form RNA. Its major groove is blocked by the phosphodiester bonds that connect the first loop residue of each hairpin with its own stem, and it is flanked by two negatively charged phosphate clusters. The loop-loop helix has alternating helical twists between adjacent base-pairs. The base-pairs at the helix junctions are overwound and three base-pairs near the helix junctions adopt high propeller twists. All these changes reduce the distance needed for the bridging phosphodiester bonds connecting each stem and loop to cross the major groove of the loop-loop helix, and result in a deformed RNA helix with localized perturbations in the minor groove surface. The alternating helical twist pattern, plus other distortions in the loop-loop helix may be important for Rom protein recognition of the kissing hairpin complex.     

基于UWB的地下定位算法和拓扑优化

地下定位面对环境恶劣、干扰、多径等影响,常规算法难以获得高精度的定位结果,同时井下环境多为狭长的巷道,不利于布置定位所需的锚节点,而井下锚节点的布置通常对定位结果有较大影响,因而使用普通的定位方法不足以满足智能采矿所需的高精度定位需求.本文对传统的三边定位算法进行分析,总结了传统三边定位结果产生误差的原因,并提出了改进的算法,通过仿真实验验证了改进算法的有效性.同时通过理论分析误差带,使用最大绝对定位误差用于仿真分析拓扑结构对定位结果精度的影响,提出了对拓扑结构的优化原则,能够根据环境特点以实现定位区域内平均最大绝对定位误差最小为原则得出最优拓扑结构.文中设置了仿真实验和实地实验对改进的算法和拓扑结构优化方法进行了验证,实验结果中,改进的算法能够在相同拓扑结构下减小15%~43%的误差,而在相同算法下优化的拓扑结构能够减小17%~65%,二者结合能够减小误差达74%.结果表明,在相同的定位条件下,改进的定位算法能够明显提高定位结果的精度,同时定位结果与拓扑结构之间也有着密切的联系,根据实际环境灵活布置拓扑结构能够使定位结果的精度进一步提高,将改进的算法与拓扑结构优化方法结合可以实现更高的定位精度.      

Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition

The crystal structure of phosphoenolpyruvate carboxylase (PEPC; EC 4. 1.1.31) has been determined by x-ray diffraction methods at 2.8-A resolution by using Escherichia coli PEPC complexed with L-aspartate, an allosteric inhibitor of all known PEPCs. The four subunits are arranged in a "dimer-of-dimers" form with respect to subunit contact, resulting in an overall square arrangement. The contents of alpha-helices and beta-strands are 65% and 5%, respectively. All of the eight beta-strands, which are widely dispersed in the primary structure, participate in the formation of a single beta-barrel. Replacement of a conserved Arg residue (Arg-438) in this linkage with Cys increased the tendency of the enzyme to dissociate into dimers. The location of the catalytic site is likely to be near the C-terminal side of the beta-barrel. The binding site for L-aspartate is located about 20 A away from the catalytic site, and four residues (Lys-773, Arg-832, Arg-587, and Asn-881) are involved in effector binding. The participation of Arg-587 is unexpected, because it is known to be catalytically essential. Because this residue is in a highly conserved glycine-rich loop, which is characteristic of PEPC, L-aspartate seemingly causes inhibition by removing this glycine-rich loop from the catalytic site. There is another mobile loop from Lys-702 to Gly-708 that is missing in the crystal structure. The importance of this loop in catalytic activity was also shown. Thus, the crystal-structure determination of PEPC revealed two mobile loops bearing the enzymatic functions and accompanying allosteric inhibition by L-aspartate.     

Secondary structure mapping of an RNA ligand that has high affinity for the MetJ repressor protein and interference modification analysis of the protein-RNA complex

The secondary structure of an RNA aptamer, which has a high affinity for the Escherichia coli MetJ repressor protein, has been mapped using ribonucleases and with diethyl pyrocarbonate. The RNA ligand is composed of a stem-loop with a highly structured internal loop. Interference modification showed that the bases within the internal loop, and those directly adjacent to it, are important in the binding of the RNA ligand to MetJ. Most of the terminal stem-loop could be removed with little effect on the binding. Ethylation interference suggests that none of the phosphate groups are absolutely essential for tight binding. The data suggest that the MetJ binding site on the aptamer is distinct from that of the natural DNA target, the 8-base pair Met box.     

基于模板的服务工作流的优化组合方法

研究了网络环境下基于模板的服务工作流的优化组合算法.该算法将服务优化组合问题转化为服务工作流模板的优化组合问题,既极大程度地复用历史服务工作流模板以减少组建新工作流的工作量,又通过优化使得服务工作流结构更为合理,缩短了服务工作流的执行时间.通过使用Petri网对网络流媒体课件制作服务工作流进行建模,并对比优化前后服务工作流模型的SPNP性能分析结果,证明了优化算法的有效性.      

Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation

The amphiphysins are brain-enriched proteins, implicated in clathrin-mediated endocytosis, that interact with dynamin through their SH3 domains. To elucidate the nature of this interaction, we have solved the crystal structure of the amphiphysin-2 (Amph2) SH3 domain to 2.2 A. The structure possesses several notable features, including an extensive patch of negative electrostatic potential covering a large portion of its dynamin binding site. This patch accounts for the specific requirement of amphiphysin for two arginines in the proline-rich binding motif to which it binds on dynamin. We demonstrate that the interaction of dynamin with amphiphysin SH3 domains, unlike that with SH3 domains of Grb2 or spectrin, prevents dynamin self-assembly into rings. Deletion of a unique insert in the n-Src loop of Amph2 SH3, a loop adjacent to the dynamin binding site, significantly reduces this effect. Conversely, replacing the n-Src loop of the N-terminal SH3 domain of Grb2 with that of Amph2 causes it to favour dynamin ring disassembly. Transferrin uptake assays show that shortening the n-Src loop of Amph2 SH3 reduces the ability of this domain to inhibit endocytosis in vivo. Our data suggest that amphiphysin SH3 domains are important regulators of the multimerization cycle of dynamin in endocytosis.     

NMR solution structure of the oxidized form of MerP, a mercuric ion binding protein involved in bacterial mercuric ion resistance

Mercuric ions are toxic to living organisms because of their strong affinity for cysteine residues in proteins. Some bacteria have developed a resistance mechanism whereby Hg2+ is transported into the cytoplasm and reduced to Hg0. One of the proteins involved in the transport of mercuric ion is the periplasmic binding protein MerP, which can exist both as oxidized (disulfide) and as reduced (dithiol) forms. Only the reduced form with Cys-17 and Cys-14 residues as free thiols is a potent receptor for mercuric ion. In this work the solution structure of the oxidized form of MerP has been determined by multidimensional NMR spectroscopy and compared to the NMR structures of the previously published structures of the reduced and mercury-bound forms of MerP. The mercury-bound and oxidized forms have similar tertiary structures, whereas in the reduced form there is a large rearrangement of the mercuric ion binding loop and the nearby loop comprising residues 38-41. The structural arrangement of the latter loop seems to be important for the stabilization of the surface location of the cysteine-containing loop. In the reduced form at low pH the cysteine-containing loop adopts a conformation similar to what is observed in the oxidized and mercury-bound forms. The oxidized form also differs with respect to the other two forms in the relative positions of some of the alpha-helices and beta-strands. Structural differences between the oxidized and reduced forms may help explain why the reduced form is stable in the periplasm, which is considered to be an oxidizing environment.     

A model of the quaternary structure of enolases, based on structural and evolutionary analysis of the octameric enolase from Bacillus subtilis

Purified enolase from Bacillus subtilis has a native mass of approximately 370 kDa. Since B. subtilis enolase was found to have a subunit mass of 46.58 kDa, the quaternary structure of B. subtilis is octameric. The pl for B. subtilis enolase is 6.1, the pH optimum (pHo) for activity is 8.1-8.2, and the Km for 2-PGA is approximately 0.67 mM. Using the dimeric Calpha structure of yeast dimeric enolase as a guide, these dimers were arranged as a tetramer of dimers to simulate the electron microscopy image processing obtained for the octameric enolase purified from Thermotoga maritima. This arrangement allowed identification of helix J of one dimer (residues 86-96) and the loop between helix L and strand 1 (HL-S1 loop) of another dimer as possible subunit interaction regions. Alignment of available enolase amino acid sequences revealed that in 16 there are two tandem glycines at the C-terminal end of helix L and the HL-S1 loop is truncated by 4-6 residues relative to the yeast polypeptide, two structural features absent in enolases known to be dimers. From these arrangements and alignments it is proposed that the GG tandem at the C-terminal end of helix L and truncation of the HL-S1 loop may play a critical role in octamer formation of enolases. Interestingly, the sequence features associated with dimeric quaternary structure are found in three phylogenetically disparate groups, suggesting that the ancestral enolase was an octamer and that the dimeric structure has arisen independently multiple times through evolutionary history.     

Optimal Stabilization of Column Buckling

Linear buckling of column structures is an important design constraint in many structures, particularly where weight is a primary concern. Active strengthening is the application of feedback control to increase the critical buckling load of the structure. An important feature of this control problem is that the structure is inherently unstable when the axial load surpasses the critical buckling load. This research presents a design method for creating optimal buckling control systems using state or static output feedback. The primary feature of this method is the ability to select the designed closed loop, actively strengthened, critical buckling load. The stability of the resulting controllers is determined using Lyapunov methods. Simulation and experimental demonstration of this algorithm is performed using a column employing piezoelectric actuators, and MEMS-based strain sensors. The optimal buckling controllers developed are able to increase the critical buckling load by a factor of 2.9. The closed loop system is able to support lower axial loads indefinitely (>30 min).     

Improved contractility and coronary flow in isolated hearts after 1-day hypothermic preservation with isoflurane is not dependent on K(ATP) channel activation

S8 is one of the core ribosomal proteins. It binds to 16 S RNA with high affinity and independently of other ribosomal proteins. It also acts as a translational repressor in Escherichia coli by binding to its own mRNA. The structure of Thermus thermophilus S8 has been determined by the method of multiple isomorphous replacement at 2.9 A resolution and refined to a crystallographic R-factor of 16.2% (Rfree 27.5%). The two domains of the structure have an alpha/beta fold and are connected by a long protruding loop. The two molecules in the asymmetric unit of the crystal interact through an extensive hydrophobic core and form a tightly associated dimer, while symmetry-related molecules form a joint beta-sheet of mixed type. This type of protein-protein interaction could be realized within the ribosomal assembly. A comparison of the structures of T. thermophilus and Bacillus stearothermophilus S8 shows that the interdomain loop is eight residues longer in the former and reveals high structural conservation of an extensive region, located in the C-terminal domain. From mutational studies this region was proposed earlier to be involved in specific interaction with RNA. On the basis of these data and on the comparison of the two structures of S8, it is proposed that the three-dimensional structure of specific RNA binding sites in ribosomal proteins is highly conserved among different species.     

Solution structure of eotaxin, a chemokine that selectively recruits eosinophils in allergic inflammation

The solution structure of the CCR3-specific chemokine, eotaxin, has been determined by NMR spectroscopy. The quaternary structure of eotaxin was investigated by ultracentrifugation and NMR, and it was found to be in equilibrium between monomer and dimer under a wide range of conditions. At pH 相似文献