Allosteric Mechanism of Calmodulin Revealed by Targeted Molecular Dynamics Simulation

Calmodulin （CAM） is involved in the regulation of a variety of cellular signaling pathways. To accomplish its physiological functions, CaM binds with Ca2＋ at its EF-hand Ca2＋ binding sites which induce the conformational switching of CaM. However, the molecular mechanism by which Ca2＋ binds with CaM and induces conformational switching is still obscure. Here we combine molecular dynamics with targeted molecular dynamics simulation and achieve the state-transition pathway of CaM. Our data show that Ca2＋ binding speeds up the conformational transition of CaM by weakening the interactions which stabilize the closed state. It spends about 6.5 ns and 5.25 ns for transition from closed state to open state for apo and holo CaM, respectively. Regarding the contribution of two EF-hands, our data indicate that the first EF-hand triggers the conformational transition and is followed by the second one. We determine that there are two interaction networks which contribute to stabilize the closed and open states, respectively.

Identification of Forcing Mechanisms of Convective Initiation over Mountains through High-Resolution Numerical Simulations

Convection and its ensuing severe weather, such as heavy rainfall, hail, tornado, and high wind, have significant im- pacts on our society and economy （e.g., Cao et al., 2004; Fritsch and Carbone, 2004; Verbout et al., 2006; Ashley and Black, 2008; Cao, 2008; Cao and Ma, 2009; Zhang et al., 2014）. Due to its localized and transient nature, the initiation of convection or convective initiation remains one of the least understood aspects of convection in the scientific communi- ties, and it is a significant challenge to accurately predict the exact timing and location of convective initiation （e.g., Cai et al., 2006; Wilson and Roberts, 2006; Xue and Martin, 2006; Cao and Zhang, 2016）.

Molecular mechanics and dynamics simulation of hydrogen diffusion in aluminum melt

The main impurities in aluminum melt are hydrogen and Al_2O_3,which can deteriorate melt quality and materials performance.However,the diffusion process of H atoms in aluminum melt and the interactions among Al atoms,Al_2O_3 and hydrogen have been studied rarely.Molecular mechanics and dynamics simulations are employed to study the diffusion behaviors of different types of hydrogen,such as free H atoms,H atoms in H_2 and H^+ions in H_2O using COMPASS force field.Correspondingly,force field types h,h1h and h1o are used to describe different types of hydrogen which are labeled as H_h,H_(h1h) and H_(h1o).The results show that the adsorption areas are maximum for H_(h1o),followed by H_(h1h) and H_h.The diffusion ability of H_(h1o) is the strongest whereas H_h is hard to diffuse in aluminum melt because of the differences in radius and potential well depth of various types of hydrogen.Al_2O_3 cluster makes the Al atoms array disordered,creating the energy conditions for hydrogen diffusion in aluminum melt.Al_2O_3 improves the diffusion of H_h and H_(h1o),and constrains H_(h1h) which accumulates around it and forms gas porosities in aluminum.H_(h1o) is the most dispersive in aluminum melt,moreover,the distance of Al-H_(h1o) is shorter than that of Al-H_(h1h),both of which are detrimental to the removal of H_(h1o).The simulation results indicate that the gas porosities can be eliminated by the removal of Al_2O_3 inclusions,and the dispersive hydrogen can be removed by adsorption function of gas bubbles or molten fluxes.

Factors influencing physical property evolution in sandstone mechanical compaction:the evidence from diagenetic simulation experiments

In order to analyze the factors influencing sandstone mechanical compaction and its physical property evolution during compaction processes, simulation exper- iments on sandstone mechanical compaction were carried out with a self-designed diagenetic simulation system. The experimental materials were modem sediments from dif- ferent sources, and the experiments were conducted under high temperature and high pressure. Results of the exper- iments show a binary function relation between primary porosity and mean size as well as sorting. With increasing overburden pressure during mechanical compaction, the evolution of porosity and permeability can be divided into rapid compaction at an early stage and slow compaction at a late stage, and the dividing pressure value of the two stages is about 12 MPa and the corresponding depth is about 600 m. In the slow compaction stage, there is a good exponential relationship between porosity and overburden pressure, while a good power function relationship exists between permeability and overburden pressure. There is also a good exponential relationship between porosity and permeability. The influence of particle size on sandstone mechanical compaction is mainly reflected in the slowcompaction stage, and the influence of sorting is mainly reflected in the rapid compaction stage. Abnormally high pressure effectively inhibits sandstone mechanical com- paction, and its control on sandstone mechanical com- paction is stronger than that of particle size and sorting. The influence of burial time on sandstone mechanical compaction is mainly in the slow compaction stage, and the porosity reduction caused by compaction is mainly con- trolled by average particle size.

Numerical simulation of spatial-temporal evolution characteristics of subsurface fluid based on strong body seismogenic model$$$$

Using finite element technique of the plane-strain problem in solid-liquid two-phase medium, we Studied the char acteristics of 'field precursors' and 'focus precursors' of subsurface fluid and their spatial-temporal evolution in case of dip-slip earthquake. The results show that: ① the change of ground fluid is slow and the anomaly is not prominent in the early period which is of elastic accumulation and non-linear; ② dilatancy emerges and anomalyfocus mainly in the source region in the moderate period which is hardening and of local dilatancy. In the period the focus precursors emerge earlier than the field precursors; ③ anomalies spreed continuously in the source area and new regions with big anomaly emerge out of the source region in the middle-short period which is of large scale dilatancy.

Numerical Simulation and Dynamical Analysis for Low Salinity Water Lens in the Expansion Area of the Changjiang Diluted Water

The low salinity water lenses（LSWLes） in the expansion area of the Changjiang diluted water（CDW） exist in a certain period of time in some years. The impact of realistic river runoff, ocean currents and weather conditions need to be taken into account in the dynamical analysis of LSWL, which is in need of research. In this paper, the POM-σ-z model is used to set up the numerical model for the expansion of the CDW. Then LSWL in summer 1977 is simulated, and its dynamic mechanism driven by wind, tide, river runoff and the Taiwan Warm Current is also analyzed. The simulated results indicate that the isolated LSWL detaches itself from the CDW near the river mouth, and then moves towards the northeast region outside the Changjiang Estuary. Its maintaining period is from July 26 to August 11. Its formation and development is mainly driven by two factors. One is the strong southeasterly wind lasting for ten days. The other is the vertical tidal mixing during the transition from neap tide to spring tide.

Numerical investigation of unsteady mixing mechanism in plate film cooling

A large-scale large eddy simulation in high performance personal computer clusters is carried out to present unsteady mixing mechanism of film cooling and the development of films. Simulation cases include a single-hole plate with the inclined angle of 30° and blowing ratio of 0.5, and a single-row plate with hole-spacing of 1.5D and 2D （diameters of the hole）. According to the massive simulation results, some new unsteady phenomena of gas films are found. The vortex system is changed in different position with the development of film cooling with the time marching the process of a single-row plate film cooling. Due to the mutual interference effects including mutual exclusion, a certain periodic sloshing and mutual fusion, and the structures of a variety of vortices change between parallel gas films. Macroscopic flow structures and heat transfer behaviors are obtained based on 20 million grids and Reynolds number of 28600.

Influence of gas transport mechanisms on the productivity of multi-stage fractured horizontal wells in shale gas reservoirs

In order to investigate the influence on shale gas well productivity caused by gas transport in nanometer- size pores, a mathematical model of multi-stage fractured horizontal wells in shale gas reservoirs is built, which considers the influence of viscous flow, Knudsen diffusion, surface diffusion, and adsorption layer thickness. A dis- crete-fracture model is used to simplify the fracture mod- cling, and a finite element method is applied to solve the model. The numerical simulation results indicate that with a decrease in the intrinsic matrix permeability, Knudsen diffusion and surface diffusion contributions to production become large and cannot be ignored. The existence of an adsorption layer on the nanopore surfaces reduces the effective pore radius and the effective porosity, resulting in low production from fractured horizontal wells. With a decrease in the pore radius, considering the adsorption layer, the production reduction rate increases. When the pore radius is less than 10 nm, because of the combined impacts of Knudsen diffusion, surface diffusion, and adsorption layers, the production of multi-stage fractured horizontal wells increases with a decrease in the pore pressure. When the pore pressure is lower than 30 MPa, the rate of production increase becomes larger with a decrease in pore pressure.

Investigation and Improvement of the Staggered Labyrinth Seal

Recent studies on staggered labyrinth seals have focused on the effects of different parameters,such as the pressure ratio and rotational speed on the leakage flow rate.However,few investigations pay sufficient attention to flow details and the sealing mechanism,which would be of practical importance in designing seals having higher performance.This paper establishes a theoretical model to study the seal mechanism,thus revealing that leakage is determined by the pressure ratio and geometric structure.Numerical simulation is implemented to illustrate details of the flow field within the seal structure.Viscous dissipation is used to quantitatively investigate the contribution that each location makes to the seal performance,revealing that orifices and stagnation points are the most important positions in the seal structure,generating the most dissipation.The orifice is carefully studied by using the theoretical model.Experiments for different pressure ratios are conducted and the results match well with those of the theoretical model and numerical simulation,verifying the theoretical model and analysis of the seal mechanism.Three new designs,based on a good understanding of the seal mechanism,are presented,with one reducing leakage by 24.5%.

Combustion mechanism development and CFD simulation for the prediction of soot emission during flaring

Industrial Flares are important safety devices to bum off the unwanted gas during process startup, shutdown, or upset. However, flaring, especially the associated smoke, is a symbol of emissions from refineries, oil gas fields, and chemical processing plants. How to simultaneously achieve high combustion efficiency （CE） and low soot emission is an important issue. Soot emissions are influenced by many factors. Flare operators tend to over-steam or over-air to suppress smoke, which results in low CE. How to achieve optimal flare performance remains a question to the industry and the regulatory agencies. In this paper, regulations in the US regarding flaring were reviewed. In order to determine the optimal operating window for the flare, different combus- tion mechanisms related to soot emissions were summar- ized. A new combustion mechanism （Vsoot） for predicting soot emissions was developed and validated against experimental data. Computational fluid dynamic （CFD） models combined with Vsoot combustion mechanism were developed to simulate the flaring events. It was observed that simulation results agree well with experimental data.

The Erosion Effect of Kapton Film in a Ground-based Atomic Oxygen Irradiation Simulator

In order to investigate the effect of space environmental factors on spacecraft materials, a ground-based simulation facility for space atomic oxygen（AO） irradiation was developed in our laboratory. Some Kapton film samples were subjected to AO beam generated by this facility. The Kapton films before and after AO exposure were analyzed comparatively using optical microscopy, scanning electronic microscopy, atomic force microscopy, high-precision microbalance, and X-ray photoelectron spectroscopy. The experimental results indicate that the transmittance of Kapton film will be reduced by AO irradiation notably, and its color deepens from pale yellow to brown. Surface roughness of the AO-treated sample is already increased obviously after AO irradiation for 5 hours, and exhibits a flannel-like appearance after 15 hours’ exposure in AO beam. The imide rings and benzene rings in kapton molecule are partially decomposed, and some new bonds form during AO irradiation. The mass loss of kapton film increases linearly with the increase of AO fluence, which is resulted from the formation of volatile products, such as CO, CO2 and NOx. The breakage in structure and degradation in properties of AO-treated Kapton film can be attributed to the integrated effect ofimpaction and oxidization of AO beam. The test results agree well with the space flight experimental data.

Effects of dipolar interactions on magnetic properties of Co nanowire arrays

Magnetic properties and magnetization processes of Co nanowire arrays with various packing densities are investigated by means of object-oriented micromagnetic framework（OOMMF） software package with finite difference micromagnetic simulations. The packing density of nanowires is changed with the diameter, number of nanowires and center-to-center spacing between the wires. The magnetization reversal mechanism and squareness of the hysteresis loops of the nanowire arrays are very sensitive to the packing density of nanowires. Clear steps and plateaux on the demagnetization are visible,which turns out that dipolar interactions among the wires have a significant influence on switching field.

Clinical Data-Driven Finite Element Analysis of the Kinetics of Chewing Cycles in Order to Optimize Occlusal Reconstructions Dedicated to Professor Karl Stark Pister for his 95th birthday

The occlusal design plays a decisive role in the fabrication of dental restorations.Dentists and dental technicians depend on mechanical simulations of mandibular movement that are as accurate as possible,in particular,to produce interference-free yet chewing-efficient dental restorations.For this,kinetic data must be available,i.e.,movements and deformations under the influence of forces and stresses.In the present study,so-called functional data were collected from healthy volunteers to provide consistent information for proper kinetics.For the latter purpose,biting and chewing forces,electrical muscle activity and jaw movements were registered synchronously,and individual magnetic resonance tomograms(MRI)were prepared.The acquired data were then added to a large complex finite element model of the complete masticatory system using the functional information obtained and individual anatomical geometries so that the kinetics of the chewing process and teeth grinding could be realistically simulated.This allows developing algorithms that optimize computer-aided manufacturing of dental prostheses close to occlusion.In this way,a failure-free function of the dental prosthesis can be guaranteed and its damage during usage can be reduced or prevented even including endosseous implants.

Effects of tilt interface boundary on mechanical properties of Cu/Ni nanoscale metallic multilayer composites

The effect of tilt interfaces and layer thickness of Cu/Ni multilayer nanowires on the deformation mechanism are investigated by molecular dynamics simulations. The results indicate that the plasticity of the sample with a 45° tilt angle is much better than the others. The yield stress is found to decrease with increasing the tilt angle and it reaches its lowest value at 33°. Then as the tilt angle continues to increase, the yield strength increases. Furthermore, the studies show that with the decrease of layer thickness, the yield strength gradually decreases. The study also reveals that these different deformation behaviors are associated with the glide of dislocation.

Quantitative Method of the Structural Damage Identification of Gas Explosion Based on Case Study:The Shanxi “11. 23” Explosion Investigation

In order to present a retrospective analysis of exposition accidents using input data from investigation processes,data from a specific accident was examined,in which we analyzed possible involved gas species（ liquefied petroleum gas; nature gas） and computed their concentrations and distributions based on the interactions between the structures and the effects of the explosion. In this study,5 scenarios were created to analyze the impact effect. Moreover,a coupling algorithm was put into practice,with a practical outflow boundary and joint strength are applied. Finally,the damage effects of each scenario were simulated. Our experimental results showed significant differences in the 5 scenarios concerning the damage effects on the building structures. The results from scenario 3 agree with the accident characteristics,demonstrating the effectiveness of our proposed modeling method. Our proposed method reflects gas properties,species and the concentration and distribution,and the simulated results validates the root cause,process,and consequences of accidental explosions. Furthermore,this method describes the evolution process of explosions in different building structures. Significantly,our model demonstrates the quantatative explosion effect of factors like gas species,gas volumes,and distributions of gases on explosion results. In this study,a feasible,effective,and quantitative method for structure safety is defined,which is helpful to accelerate the development of safer site regulations.

Modeling and simulation of temperature control system in plant factory using energy balance

Closed production systems,such as plant factories and vertical farms,have emerged to ensure a sustainable supply of fresh food,to cope with the increasing consumption of natural resource for the growing population.In a plant factory,a microclimate model is one of the direct control components of a whole system.In order to better realize the dynamic regulation for the microclimate model,energy-saving and consumption reduction,it is necessary to optimize the environmental parameters in the plant factory,and thereby to determine the influencing factors of atmosphere control systems.Therefore,this study aims to identify accurate microclimate models,and further to predict temperature change based on the experimental data,using the classification and regression trees(CART)algorithm.A random forest theory was used to represent the temperature control system.A mechanism model of the temperature control system was proposed to improve the performance of the plant factories.In terms of energy efficiency,the main influencing factors on temperature change in the plant factories were obtained,including the temperature and air volume flow of the temperature control device,as well as the internal relative humidity.The generalization error of the prediction model can reach 0.0907.The results demonstrated that the proposed model can present the quantitative relationship and prediction function.This study can provide a reference for the design of high-precision environmental control systems in plant factories.

A NUMERICAL SIMULATION OF 3-D INNER FLOW IN UP-STREAM PUMPING MECHANICAL SEAL

Numerical simulation of 3-D inner flow between Up-stream Pumping Mechanical Face Seals （UPMFS） faces was initially done by CFD software, which made the flow visualization come true. Simulation results directly discover the action of hydrodynamic lubrication, and by comparison with that of Conventional Mechanic Face Seals （CMFS）, the advantage over bigger bearing capability, less friction and much less leakage are explained clearly. Otherwise there are also some different ideas and results from precedent analysis and computational research results： dynamic and static pressure profiles can be obtained respectively instead of the analytic total pressure distribution only, pressure distribution is nonlinear, while always be solved as linear, lower pressure is observed at the area of inner diameter caused by the grooves, but its possible cavitations effects to the performance of UPMFS still need further study.

Local melting mechanism and its effects on mechanical properties of friction spot welded joint for Al-Zn-Mg-Cu alloy

Local melting and the eutectic film and liquation crack formation mechanisms during friction spot weld- ing （FSpW） of Al-Zn-Mg-Cu alloy were studied by both experiment and finite element simulation. Their effects on mechanical properties of the joint were examined. When the welding heat input was high, the peak temperature in the stir zone was higher than the incipient melting temperature of the Al-Zn-Mg-Cu alloy. This resulted in local melting along the grain boundaries in this zone. In the retreating stage of the welding process, the formed liquid phase was driven by the flowing plastic material and redistributed as a ＂U-shaped＂ line in the stir zone. In the following cooling stage, this liquid phase transformed into eutectic films and liquation cracks. As a result, a new characteristic of＂U＂ line that consisted of eutectic films and liquation cracks is formed in the FSpWjoin. This ＂U＂ line was located in the high stress region when the FSpW joint was loaded, thus it was adverse to the mechanical properties of the FSpW joint. During tensile shear tests, the ＂U＂ line became a preferred crack propagation path, resulting in the occurrence of brittle fracture.

Micromechanical Behavior and Failure Mechanism of F / B Multi-phase High Performance Steel

The deformation and micro-voids formation mechanisms in ferrite / bainite（ F / B） multi-phase steel with the volume fraction of bainite less than 50% were studied by numerical simulation and experimental observation. The results show that the micro-strain concentrates at the soft / hard phase（ F / B） interface in the multi-phase steel,which should be correlated with the mechanism of incoordinate deformation. During the necking of the steel,the micro-voids initially form around the F / B interface,which also form in ferrite and bainite with the severe strain. The micro-voids in bainite are more dense and finer than those in ferrite. The failure mechanism of bainite is the coalescence of micro-voids,and the failure mechanism of ferrite is the growth and tearing of micro-voids. Due to the different failure mechanisms of ferrite and bainite,a suitable part of soft phase would be beneficial to the capability of anti-failure of F / B multi-phase steel during the ductile fracture.

An empirical description for the hinge-like mechanism in single-layer black phosphorus:The angle–angle cross interaction

The single-layer black phosphorus is characterized by its puckered configuration that pos- sesses the hinge-like behavior, which leads to the highly anisotropic in-plane Poisson＇s ratios and the negative out-of-plane Poisson＇s ratio. We demonstrate that the hinge-like mechanism can be described by the angle-angle cross interaction, which, combined with the bond stretching and angle bending interactions, is able to provide a good description for the mechanical properties of single-layer black phosphorus. We also propose a nonlinear angle-angle cross interaction, which follows the form of Stillinger-Weber potential and can be advantageous for molecular dynamics simulations of single-layer black phosphorus under large deformation.