Thermodynamical properties of protein kinase with adenine inhibitors

The protein-based molecular recognition of the adenine ring is essential to understand protein function and drug design as well.In this paper,a variety of the adenine-based inhibitors with modified groups of amino groups,nitrogen and oxygen atoms in the aromatic ring are designed,and the binding capability of these adenosine analogues with an aminoglycoside antibiotic kinase [APH(3’)-IIIa] are investigated with activity assays and isothermal titration calorimetry(ITC) experiments.1-aminoisoquinoline is one of the weakest substrates bound to APH(3’)-IIIa with the lowest affinity(high ki and high kd) and the smallest negative value of free energy change(G) among the inhibitors tested.The binding process of adenine and 5-nitroisoquinoline to APH(3’)-IIIa is an enthalpy-driven event with unfavorable entropy,which is consistent with the energy change induced by the binding of ATP to the enzyme.However,the reverse is true for 1-aminoisoquinoline,3-amino-5-nitrobenzisothiazole,5-aminoisoquinoline binding to the enzyme because the entropy is more favorable and the enthalpy makes a lower contribution to the binding process.These results suggest that small changes of the adenine ring can lead to significant influence on the ability of these analogues to occupy the adenine-binding region of the enzyme,which can be the potential inhibitors as drug candidates against the bacterial resistance.     

Testing and Modeling for Energy Dissipation Behavior of Velocity and Displacement Dependent Hydraulic Damper

A passive energy-dissipating device, velocity, and displacement dependent hydraulic damper (VDHD), is developed to reduce the seismic response of structure. This device is comprised of a hydraulic jack, check valve, relief valve, and throttle valve. The numerical analysis model for SAP2000 nonlinear analysis program is proposed to simulate the energy-dissipating characteristics of VDHD. The analysis results of this model compared with the seismic resistant tests reveal that this proposed model can accurately describe the actual energy-dissipating behavior of VDHD. The efficiency of VDHD is confirmed using this proposed model for carrying out numerical analyses of bare building, building added with bulking resistant bracing (BBR), and VDHD. The energy-dissipating capabilities of VDHD are performing excellent displacement and acceleration control with various ground magnitudes; being an energy absorber to absorb mechanical energy in the structure and resist structural movement; and gathering the advantage of BRB.     

Information Model for Connection Management in Automatic Switched Optical Network

The three types of connections (Permanent Connection, Soft Permanent Connection and Switched Connection) provided by ASON can adapt the requirement of different network services. Management and maintenance of these three connections are the most important aspect of ASON management. The information models proposed in this paper are used for the purpose of ASON connection management. Firstly a new information model is proposed to meet the requirement for the control plane introduced by ASON. In this model, a new class ControlNE is given, and the relationship between the ControlNE and the transport NE (network element) is also defined. Then this paper proposes information models for the three types of connections for the first time, and analyzes the relationship between the three kinds of connections and the basic network transport entities. Finally, the paper defines some CORBA interfaces for the management of the three connections. In these interfaces, some operations such as create or release a connection are defined, and some other operations can manage the performance of the three kinds of connections, which is necessary for a distributed management system.     

Adsorption Equation and Adsorption Paramenter of Cellulase to Cellulose Fibres in Biofinishing

Adsorption isotherms for SF cellulase from Trichoderma pseudokoningii on cotton, flax and viscose yarns were investigated to provide information about cellulase-cellulose binding on different types of cellulosic fibres. The half-saturation constants and maximum adsorption constants suggest that SF cellulase has greater affinity for viscose than for cotton and greater affinity for cotton than for flax. It is suggested that this is related to the different crystallinities and microporous structures of these fibre types. The fraction of adsorbable protein in the total cellulase was found to be the same for each of the three cellulase substrates.     

Rigorous Modeling of Real-time System Based on UML and PVS

Rigorous modeling could improve the correctness and reduce cost in embedded real-time system development for models could be verified. Tools are needed for rigorous modeling of embedded real-time system. UML is an industrial standard modeling language which provides a powerful expressi-veness, intuitive and easy to use interface to model. UML is widely accepted by software developer. However, for lack of precisely defined semantics, especially on the dynamic diagrams, UML model is hard to be verified. PVS is a general formal method which provides a high-order logic specification language and integrated with model checking and theorem proving tools. Combining the widely used UML with PVS, this paper provides a novel modeling and verification approach for embedded real-time system. In this approach, we provide 1) a timed extended UML statechart for modeling dynamic behavior of an embedded real-time system; 2) an approach to capture timed automata based semantics from timed statechart; and 3) an algorithm to generate a finite state model expressed in PVS specification for model checking. The benefits of our approach include flexible and friendly in modeling, extendable in formalization and verification content, and better performance. Time constraints are modeled and verified and its a highlight of this paper.     

Analysis of the global T_m–T_s correlation and establishment of the latitude-related linear model

In this study,the correlation between Tm,a key variable in GNSS water vapor inversion,and surface temperature(Ts)was calculated on a global scale based on the global geodetic observing system(GGOS)atmosphere Tmdata and European centre for medium-range weather forecasts(ECMWF)surface temperature data.The results show that their correlation is mainly affected by latitudes,and the correlation is stronger at high latitudes and weaker at low latitudes.Although the correlation is relatively weak in the tropic areas,the temperature changes so little in a year in these areas that we can still achieve good Tmresults by linear regression model.Based on these facts,‘‘GGOS atmosphere’’Tmdata and ECMWF Tsdata from 2005 to2011 were used to establish the global latitude-related linear regression model.The new model has root mean square error(RMSE)of 3.2,3.3,and 4.4 K,respectively,compared with respect to the‘‘GGOS atmosphere’’data,COSMIC data,and radiosonde data and is more accurate than the Bevis Tm–Tsrelationship.     

Markov Graph Model Computation and Its Application to Intrusion Detection

Markov model is usually selected as the base model of user action in the intrusion detection system （IDS）. However, the performance of the IDS depends on the status space of Markov model and it will degrade as the space dimension grows. Here, Markov Graph Model （MGM） is proposed to handle this issue. Specification of the model is described, and several methods for probability computation with MGM are also presented. Based on MGM, algorithms for building user model and predicting user action are presented. And the performance of these algorithms such as computing complexity, prediction accuracy, and storage requirement of MGM are analyzed.     

Establishment of a new dynamic RRC model in smoke toxicity evaluation and engineering application

It is by now a well established fact that the overwhelming hazard from fire is smoke as far as the death of people in the fire is concerned. There are many methodologies for addressing the smoke toxicity component of fire hazard such as CO stochastic model,FED (fractional effective dose) model, FEC (fractional effective concentration) model, N-gas model and so on. None of these models can reflect spatio-temporal variation of the smoke concentration. A new dynamic smoke toxicity evaluation model, RRC (respiration, route and concentration) model, is proposed in this paper concerning the three decisive factors in real fire such as the respiration, movement route of people and the distribution of smoke concentration in the building. Furthermore, an example of the model is presented.     

Earthquake Resistant Engineering and Application of Seismic Zonation Map of China

China is a country with high seismieity. It is very important for industry and structure to fortify against earthquakes. In this paper the outline of seismicity in China, the criteria for fortification against earthquakes and the contents of seismic zonation map of China are described. The contents of seismic safety evaluation for major construction projects, such as large dams, large bridges, long distance pipe lines for transporting oil and natural gas, nuclear plants, petrochemical enterprises and so on, are presented. Some geological disasters caused by destructive earthquake, such as earthquake-caused collapse and landslide, liquefaction of saturated soll and earthquake fault and so on, are also presented. Preventive countermeasures for these disasters are discussed.     

Combining docking and comparative molecular similarity indices analysis （COMSIA） to predict estrogen activity and probe molecular mechanisms of estrogen activity for estrogen compounds

Estrogen compounds are suspected of disrupting endocrine functions by mimicking natural hormones, and such compounds may pose a serious threat to the health of humans and wildlife. Close attention has been paid to the prediction and molecular mechanisms of estrogen activity for estrogen com- pounds. In this article, estrogen receptor a subtype （ERa） -based comparative molecular similarity indices analysis （COMSIA） was performed on 44 estrogen compounds with structural diversity to find out the structural relationship with the activity and to predict the activity. The model with the significant correlation and the best predictive power （R^2= 0.965, Q^2 LOO： 0.599, R^2 pred ： 0.825） was achieved. The COMSIA and docking results revealed the structural features for estrogen activity and key amino acid residues in binding pocket, and provided an insight into the interaction between the ligands and these amino acid residues.     

Study on the specific interaction between angiogenin and aptamer by atomic force microscopy （AFM）

The specific interaction between angiogenin and aptamer has been investigated by using AFM. The specificity of the interaction is revealed by comparing the binding probability of aptamer to other elements in a series of control experiments. The results have shown that there is specific interaction force between angiogenin and aptamer. Moreover, the single molecular pull-off force between angiogenin and aptamer has also been determined using the Poisson statistical method to be 133.7±11.7 pN. These findings obtained are helpful to the better revelation of recognition mechanism between angiogenin and aptamer, which provided basis for further understanding the inhibition of the aptamer to angiogenic activity.     

Improving analytic hierarchy process applied to fire risk analysis of public building

The structure importance in Fault Tree Analysis (FTA) reflects how important Basic Events are to Top Event. Attribute at alternative level in Analytic Hierarchy Process (AHP) also reflect its importance to general goal. Based on the coherence of these two methods, an improved AHP is put forward. Using this improved method, how important the attribute is to the fire safety of public building can be analyzed more credibly because of the reduction of subjective judgment. Olympic venues are very important public buildings in China. The fire safety evaluation of them will be a big issue to engineers. Improved AHP is a useful tool to the safety evaluation to these Olympic venues, and it will guide the evaluation in other areas. Support by the National Natural Science Foundation of China (Grant No. 50536030), National Project of Scientific and Technical Supporting Programs funded by Ministry of Science & Technology of China (Grant No. 2006BAK06B02) and China Postdoctoral Science Foundation (Grant No. 20070410220)     

Microstructure and structural color in wing scales of butterfly Thaumantis diores

The butterfly Thaumantis diores is a species in the Northeast of China. There are two kinds of scales on its wings, which overlap like roof tiles and completely cover the membrane. The SEM results showed that only Type-I scales play a key role in forming the blue structural color. Type-II scales have black chemical color. The cross section micro-configuration of scales is achieved by using the transmission electron microscopy (TEM). The brilliant blue generated through the multilayer microstructure is explained by the photonic crystal reason. The multilayer microstructure of the ridges is optimized to 1D Bragg stack for simulation. The reflectivity of the wing is measured by a spectrometer, and the experimental graph accord with the simulation curves basically. When this species fly, the wing’s color and brightness can change because of the transform between structural color and chemical color. The bionic color-changing design and the significance of this effect in video stealth or other fields are discussed at the end of the paper. Supported by Fok Ying Tong Education Foundation (Grant No. 101020), the Natural Science Foundation of China (Grant No. 30570235, 50635030), National Basic Research of China (Grant No. 2007CB616913) and Key Project of the Ministry of Education (Grant No. 105059)     

An analysis of soil composition and mechanical properties of riverbanks in a braided reach of the Lower Yellow River

The channel adjustment in a braided reach is very prominent in the fluvial processes of the Lower Yellow Rlver, In whlch the process of bank erosion plays an important role, especially durlng the perlod of clear water scourlng. The process of bank erosion is closely related to soil composition and mechanlcal properties of the riverbanks. In this paper, the recent bank erosion process in a bralded reach between Huayuankou and Gaocun was firstly investigated after the water impoundment and sediment detentlon of the Xlaolangdi Reservoir, and then a field observation and indoor soil testa were conducted at 10 typlcal riverbanks in the braided reach. Through analyzing the experlmental results, changes of t;brtnsml-soo; composition and mechanical properties were found, and the two real reasons causlng serlous bank erosion in the braided reach were identified. The following conclusions were drawn from thls study： （i） the majority of riverbanks are made up of cohesive soil, and can be characterlzed by obvlous vertlcal stratification structures of soil composition; （ii） these riverbanks are very erodlble due to the lower clay-content and weak erosion-resistant strength in the bank soil, wlth its crltlcal shear stress value （0.1-0.3 Pa） being much less than that of the average near-bank flow shear stress （2.0-3.0 Pa）, which is one important reason causing serious bank erosion; （iii） frequent occurrence of bank fallure during flood seasons usually results from the fact that the values of shear strength parameters such as the cohesion and internal friction angle decrease with the increase of water content In riverbank soil, and the value of cohesion reduces drastically from 34 to 4 kPa wlth the Increase of water content, which is another important reason causing serious bank erosion in the bralded reach.     

Influence of location-dependent protuberance damage on cell viability

The influence of femtosecond laser-induced damages on viability of olfactory ensheathing cells (OECs) is investigated. Several cytokinetic processes including cellular damage, recovery and death are discussed. Using femtosecond laser with the power of 100 μW and cutting speed of 2 μm/s, we cut the cellular protuberance with smaller diameter twice in different locations, and then observe the viability of the damaged cells. Under the same conditions, the root of protuberance with larger diameter is cut six times to observe changes of cellular shape. Whether the damage is located in the end, middle or root of protuberance with smaller diameter, the cell viability can recover within 3 h. When the damage is located in the root of protuberance with larger diameter, the damaged cell will die in the way of oncosis. Cytokinetic phenomena including intracellular high Ca²⁺ concentration, cellular morphologic change, recovery and oncosis are discussed. Meanwhile, high Ca²⁺ concentration is observed after femtosecond laser surgery. Therefore, femtosecond laser surgery is an important tool for establishing cell damage model and studying cytokinetics. Supported by National High Technology Research & Development Program of China (Grant No. 2006AA04Z307), Author of National Excellent Doctoral Dissertation of PR China (Grant No. 2006039), National Natural Science Foundation of China (Grant No. 50775104), Natural Science Foundation of Jiangsu Province (Grant No. BK2006507) and Jiangsu Provincial Research Innovation Program for College Graduates (Grant No. CX07B_086z)     

Crack spacing of unsaturated soils in the critical state

The cracking mechanism of unsaturated soils due to evaporation is poorly understood, and the magnitude of crack spacing is usually hard to estimate. In this work, cracks were postulated to occur succedently rather than simultaneously, that is, secondary cracks appear after primary cracks as evaporation continues. Formulae of the secondary crack spacing and secondary trend crack spacing were then derived after stress analysis. The calculated spacing values were consistent with the published experimental data. Meanwhile, the effect of the Poisson ratio on the crack spacing was analyzed, which showed that the magnitude of crack spacing was proportional to the Poisson ratio in the range of [0.30, 0.35].     

Hardness of materials: studies at levels from atoms to crystals

Based on the electron-holding energy per unit volume, we extend the concept of hardness to atomic stiffness, ionic stiffness and bond hardness, investigating the nature of material hardness at these three levels. We find that the stiffness of isolated atoms or ions has no direct connection with the hardness of materials, whereas material hardness is directly related to bond hardness, which is essentially determined by the electron-holding energy of its constituent chemical bonds per unit volume. We establish a model for identifying the hardness of materials on the basis of bond hardness. This work offers a deeper understanding of the nature of material hardness at the atomic level, and provides a practical guide in the search for new superhard materials. Supported by National Natural Science Foundation of China (Grant No. 20471012), Program for New Century Excellent Talents in University (Grant No. NCET-05-0278) and Foundation for the Author of National Excellent Doctoral Dissertation of China (Grant No. 200322)     

Crystal structures of catalytic and regulatory subunits of rat protein kinase CK2

Protein kinase CK2 consists of two catalytic subunits (CK2α) and two regulatory subunits (CK2β). Here, we report the crystal structures of rat CK2α mutant (rCK2α-△C, 1—335) and CK2β (rCK2β). The overall topology of rCK2α-△C and rCK2β are very similar to the human enzyme, although large structural differences could be observed in the N-terminal domain of rCK2α-△C. Our reported structure of rCK2α-△C is in the close conformation state while the counterpart hCK2α is in the open conformation state, indi- cating ...     

Effect of the contact distance on transport properties of an orsanic molecular device

Using a spatially symmetric phenyldithiolate molecule sandwiched between two gold electrodes as model system and through shifting one electrode from symmetric contact site to form asymmetric contact, we investigated the properties of electronic transport in such a device by the first-principles. It was found that the/（G ）-V characteristics of a device show significant asymmetry and the magnitudes of current and conductance depend remarkably on the variation of molecule-metal distance at one of the two contacts. Namely, an asymmetric contact would lead to the weak rectifying effects on the current-voltage characteristics of a molecular device. The analysis shows that the HOMO is responsible for the resonant tunneling and its shift due to the charging of the device while the bias voltage is the intrinsic origin of asymmetric/（G）- Vcharacteristics.