Towards dynamic structure of biological complexes at atomic resolution by cryo-EM

Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.

Dynamic Structure of Mo-O Species in Ag-Mo-P-O Catalyst for Oxidative Dehydrogenation of Propane

The dynamic structure of Mo-O species in Ag-Mo-P-O catalyst was studied by in situ confocal microprobe laser Raman spectroscopy (LRS) and catalytic test. The results indicate Mo-O species of MoO3 transformed to Mo-O species of AgMoO2PO4 in C3H8/O2/N2 (3/1/4) flow at 773 K. This behavior is closely relative to oxidative dehydrogenation of propane and intrinsic properties of Mo-O species. The Mo-O species of AgMoO2PO4 may be active species for oxidative dehydrogenation of propane.

Seismic response of a mid-story isolated structure considering SSI in mountainous areas under long-period earthquakes

At present,there is not much research on mid-story isolated structures in mountainous areas.In this study,a model of a mid-story isolated structure considering soil-structure interaction(SSI)in mountainous areas is established along with a model that does not consider SSI.Eight long-period earthquake waves and two ordinary earthquake waves are selected as inputs for the dynamic time history analysis of the structure.The results show that the seismic response of a mid-story isolated structure considering SSI in mountainous areas can be amplified when compared with a structure that does not consider SSI.The structure response under long-period earthquakes is larger than that of ordinary earthquakes.The structure response under far-field harmonic-like earthquakes is larger than that of near-fault pulse-type earthquakes.The structure response under near-fault pulse-type earthquakes is larger than that of far-field non-harmonic earthquakes.When subjected to long-period earthquakes,the displacement of the isolated bearings exceeded the limit value,which led to instability and overturning of the structure.The structure with dampers in the isolated story could adequately control the nonlinear response of the structure,effectively reduce the displacement of the isolated bearings,and provide a convenient,efficient and economic method not only for new construction but also to retrofit existing structures.

Dynamic structure change of Cu nanoparticles on carbon supports for CO_(2) electro-reduction toward multicarbon products

Cu nanoparticles with different sizes,morphology,and surface structures exhibit distinct activity and selectivity toward CO_(2) reduction reaction,while the reactive sites and reaction mechanisms are very controversial in experiments.In this study,we demonstrate the dynamic structure change of Cu clusters on graphite-like carbon supports plays an important role in the multicarbon production by combining static calculations and ab-initio molecular dynamic simulations.The mobility of Cu clusters on graphite is attributed to the near-degenerate energies of various adsorption configurations,as the interaction between Cu atoms and surface C atoms is weaker than that of Cu-Cu bonds in the tight cluster form.Such structure change of Cu clusters leads to step-like irregular surface structures and appropriate interparticle distances,increasing the selectivity of multicarbon products by reducing the energy barriers of C-C coupling effectively.In contrast,the large ratio of edge and corner sites on Cu clusters is responsible for the increased catalytic activity and selectivity for CO and H_(2) compared with Cu(100)surface,instead of hydrocarbon products like methane and ethylene.The detailed study reveals that the dynamic structure change of the catalysts results in roughened surface morphologies during catalytic reactions and plays an essential role in the selectivity of CO_(2) electro-reduction,which should be paid more attention for studies on the reaction mechanisms.

Effects of three-body interaction on dynamic and static structure factors of an optically-trapped Bose gas

We investigate how three-body interactions affect the elementary excitations and dynamic structure factor of a Bose- Einstein condensate trapped in a one-dimensional optical lattice. To this end, we numerically solve the Gross-Pitaevskii equation and then the corresponding Bogoliubov equations. Our results show that three-body interactions can change both the Bogoliubov band structure and the dynamical structure factor dramatically, especially in the case of the two-body interaction being relatively small. Furthermore, when the optical lattice is strong enough, the analytical results, combined with the sum-rule approach, help us to understand that： the effects of three-body interactions on the static structure Ihctor can be significantly amplified by an optical lattice. Our predictions should be observable within the current Bragg spectroscopy experiment.

An Application of Dynamic Structure Model to SoilCorrosion Research

Soil corrosion is a complex system which is difficult to be simulated with mathematicalmodels. Taking the mountainous areas in western henan Province as an example, this paper describesthe application of dynamic structure model to soil corrosion analysis. The primary component factors ofthe soil corrosion system and the causality of the factors are determined in this paper. The interactiverelations of the systematic variables is established with delphi method. The dynamic structure modelis selected to make the forecast of the soil corrosion system, the analysis of sensitivity of the variablesand the analysis of the system control.

Specification of dynamic structure discrete event systems using single point encapsulated control functions

In Discrete Event System Specification(DEVS),the dynamics of a network is constituted only by the dynamics of its basic components.The state of each component is fully encapsulated.Control in the network is fully decentralized to each component.At dynamic structure level,DEVS should permit the same level of decentralization.However,it is hard to ensure structure consistency while letting all components achieve structure changes.Besides,this solution can be complex to implement.To avoid these difficulties,usual dynamic structure approaches ensure structure consistency allowing structure changes to be done only by the network having newly added dynamics change capabilities.This is a safe and simple way to achieve dynamic structure.However,it should be possible to simply allow components of a network to modify the structure of their network,other components and/or their own structure—without having to modify the usual definition a DEVS network.In this manuscript,it is shown that a simple fully decentralized approach is possible while ensuring full modularity and structure consistency.

Responses of thermal structure and vertical dynamic structure of South China Sea to Typhoon Chanchu

The response of the South China Sea（SCS） to Typhoon Chanchu（2006） was examined using the MM5 and POM model. In the POM model, sea surface boundary conditions were forced by the simulation wind field from MM5, the velocity forcing was introduced in the eastern boundary and the computational schemes of heat fluxes at the surface were introduced. Comparison with the observation data shows that the simulated results are reliable. In the response process of the SCS to Typhoon Chanchu, the influence of the heat fluxes on thermal structure of the SCS was regionally different. Strong wind forcing would lead to upwelling phenomenon in the lateral boundary of deep water basin. Furthermore, the Ekman pumping theory was used to discuss subsurface upwelling and downwelling phenomenon in typhoon forced stage.

The Dynamical Characteristics and Wave Structure of Typhoon Rananim (2004)

Typhoon Rananim （2004） was one of the severest typhoons landfalling the Chinese mainland from 1996 to 2004. It brought serious damage and induced prodigious economical loss. Using a new generation of mesoscale model, named the Weather Research and Forecasting （WRF） modeling system, with 1.667 km grid horizontal spacing on the finest nested mesh, Rananim was successfully simulated in terms of track, intensity, eye, eyewall, and spiral rainbands. We compared the structures of Rananim to those of hurricanes in previous studies and observations to assess the validity of simulation. The three-dimensional （3D） dynamic and thermal structures of eye and eyewall were studied based on the simulated results. The focus was investigation of the characteristics of the vortex Rossby waves in the inner-core region. We found that the Rossby vortex waves propagate azimuthally upwind against the azimuthal mean tangential flow around the eyewall, and their period was longer than that of an air parcel moving within the azimuthal mean tangential flow. They also propagated outward against the boundary layer inflow of the azimuthal mean vortex. Puthermore, we studied the connection between the spiral potential vorticity （PV） bands and spiral rainbands, and found that the vortex Rossby waves played an important role in the formation process of spiral rainbands.

F-structure model of overlying strata for dynamic disaster prevention in coal mine

The rupture and movement scope of overlying strata upon the longwall mining face increased sharply as the exploitation scale and degree growing recently,and the spatial structure formed by fractured strata became much more complex.The overlying strata above the working face and adjacent gobs would affect each other and move cooperatively because small pillar can hardly separate the connection of overlying strata between two workfaces,which leads to mining seismicity in the gob and induces rockburst disaster that named spatial structure instability rockburst in this paper.Based on the key stratum theory,the F-structure model was established to describe the overlying strata characteristic and rockburst mechanism of workface with one side of gob and the other side un-mined solid coal seam.The results show that F-structure in the gob will re-active and loss stability under the influence of neighboring mining,and fracture and shear slipping in the process of instability is the mechanism of the seismicity in the gob.The F-structure was divided into two categories that short-arm F and long-arm F structure based on the state of strata above the gob.We studied the underground pressure rules of different F-structure and instability mechanism,thus provide the guide for prevention and control of the F-structure spatial instability rockburst.The micro-seismic system is used for on-site monitoring and researching the distribution rules of seismic events,the results confrmed the existence and correct of F-spatial structure.At last specialized methods for prevention seismicity and rockburst induced by F-structure instability are proposed and applied in Huating Coal Mine.

FUNDAMENTAL OF DYNAMICAL ANALYSIS OF THE BLAST-RESISTANT UNDERGROUND STRUCTURES

In this paper, the generalized variational principle of dynamic analysis for the blast-resistant underground structures is established, and the corresponding generalized functional of elastoplastic analysis for underground structures is derived, and the generalized variational principle of nonconservative system is given, thus the fundamental of dynamical analysis for underground structures to resist blast is proposed. Finally, for the underground cylindrical structure to resist blast, dynamical calculations are made, and compared with the test results.

ANALYSIS OF DYNAMIC STABILITY OF SUBMERGED STRUCTURE

The submerged structure is basically a large three-dimensional structure of few statically redundant members. The structure is subjected to vertical dead and live loads in addition to the wave forces. An analysis of dynamic stability of the submerged structure without damping has been made by J. Thomas and Abbas (1980). In this paper the analyses of dynamic stability of the sumberged structure with damping are conducted. The case structure with damping is more complicated 'than the case without it. According to the principle of perturbation, a new model for dynamic stability calculation in consideration of damping effect is developed. In this paper, the formulas are deduced, the computational program is compiled, the practical examples are analysed, and this problem is solved very satisfactorily. The computational results show that the shape and value of the regions of dynamic instability can be changed significantly by damping. So only by considering damping can the property of dynamic stability of the submerged structure be reflected correctly.

Dynamical Model Updating Based on Modal Tests with Changed Structure

A new approach to modifying the stiffness and mass matrices of finite element models is presented to improve the calculation precision.By measuring the mode frequencies and shapes of both of the original and the new structures with changed stiffness and mass,the stiffness and mass matrices of the finite element model can be updated through matrices calculation and solving algebra equations.Taking a multi-freedom model as an example,the relation between the number of the modes and the correction precision of stiffness and mass matrix elements is researched.The facility and precision of the method are totally confirmed especially when the modeling error is known limited to a definite local range.The feasibility of the approach is proven by an effective engineering application to the model updating of a wing piece used in flutter test.

Numerical Simulation of ATPS Parachute Transient Dynamics Using Fluid-Structure Interaction Method

In order to simulate and analyze the dynamic characteristics of the parachute from advanced tactical parachute system(ATPS),a nonlinear finite element algorithm and a preconditioning finite volume method are employed and developed to construct three dimensional parachute fluid-structure interaction(FSI)model.Parachute fabric material is represented by membrane-cable elements,and geometrical nonlinear algorithm is employed with wrinkling technique embedded to simulate the large deformations of parachute structure by applying the NewtonRaphson iteration method.On the other hand,the time-dependent flow surrounding parachute canopy is simulated using preconditioned lower-upper symmetric Gauss-Seidel(LU-SGS)method.The pseudo solid dynamic mesh algorithm is employed to update the flow-field mesh based on the complex and arbitrary motion of parachute canopy.Due to the large amount of computation during the FSI simulation,massage passing interface(MPI)parallel computation technique is used for all those three modules to improve the performance of the FSI code.The FSI method is tested to simulate one kind of ATPS parachutes to predict the parachute configuration and anticipate the parachute descent speeds.The comparison of results between the proposed method and those in literatures demonstrates the method to be a useful tool for parachute designers.

DYNAMIC OPTIMIZATION OF THERMAL STRUCTURE

he temperature distnbution on the surface of a flight vehicle and the va-riation of the modulus of elasticity with respect to temperature are considered. The minimum weight structural design with constraints on frequency, on the coordinates ofmodal nodes and on the upper and lower bounds of the design vanables are studied us-ing Kuhn-Tucker conditions as optimal cntenon. The vanation of the flrst three ordernatural frequencies, modal shapes and minimum structural weight vs temperature gra-dient are discussed. It is pointed out that it is imperative to take into account the effectof aerodynamic heating on structural dynamic optimization. Calculation example showsthat the method obtained is feasible and efficient.

Dynamic Balancing Structure Optimal Design for the Rotating Arc Sensor

Rotating arc sensor is a key device for automation welding. The vibration has a big influence on signal's correct collection and reliable automatic welding. In order to solve the vibration problem and the dynamic balancing design with the restricted space,a bearing force analysis based dynamic balancing structure optimal design is proposed and implemented with the help of Pro/Engineer( PROE) and automatic dynamic analysis of mechanical systems( ADAMS) virtual prototype technology, in which three parameters of the counterbalance are considered. The method is suitable for the practical online adjustment. The simulation result shows that optimal design based counterbalance structure and parameters can satisfy the space requirement with lower vibration. The methodology provides a new idea for dynamic balancing design and adjustment of rotating arc sensor with adjustable rotation radius.

Volatility Structures of ForwardRates and the Dynamics of the TermStructure:a Multifactor Case

For general volatility structures for forward rates, the evolution of interest rates may not be Markovian and the entire path may be necessary to capture the dynamics of the term structure. This article identifies conditions on the volatility structure of forward rates that permit the dynamics of the term structure to be represented by a finite-dimensional state variable Markov process. In the deterministic volatility case, we interpret then-factor model as a sum ofn unidimensional models.

Non-monotonic temperature evolution of nonlocal structure–dynamics correlation in CuZr glass-forming liquids

The structure–dynamics correlations in a nonlocal manner were investigated in CuZr metallic glass-forming liquids via classical molecular dynamics simulations.A spatial coarse-graining approach was employed to incorporate the nonlocal structural information of given structural order parameters in the structure–dynamics relationship.It is found that the correlation between structure order parameters and dynamics increases with increasing coarse-graining length and has a characteristic length scale.Moreover,the characteristic correlation length exhibits a non-monotonic temperature evolution as temperature approaches glass transition temperature,which is not sensitive to the considered structure order parameters.Our results unveil a striking change in the structure–dynamics correlation,which involves no fitting theoretical interpretation.These findings provide new insight into the structure–dynamics correlation in glass transition.

DYNAMIC RESPONSE OF UNDERGROUND STRUCTURES BY TIME DOMAIN SBEM AND SFEM

The dynamic interaction problems of three-dimensional lineqr elastic structures with arbitrary shaped section embedded in a homogeneous, isotropic and linear elastic half space under dynamic disturbances are numerically solved. The numerical method employed is a combination of the time domain semi-analytical boundary element method (SBEM) used for the semi-infinite soil medium and the semi-analytical finite element method (SFEM) used for the three-dimensional structure. The two methods are combined through equilibrium and compatibility conditions at the soil-structure interface. Displacements, velocities, accelerations and interaction forces at the interface between underground structure and soil medium produced by the diffraction of wave by an underground structure for every time step are obtained. In dynamic soil-structure interaction problems, it is advantageous to combine the SBEM and the SFEM in an effort to produce an optimum numerical hybrid scheme which is characterized by the main advantages of the two methods. The effects of the thickness, the ratio of length and diameter of underground structure and the soil medium on dynamic responses are discussed.