Computational Simulation of Aptamer-target Binding Mechanisms

Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.

Exploration of instantaneous frequency for local control assessment in real-time hybrid simulation

Local control parameters such as instantaneous delay and instantaneous amplitude play an essential role in evaluating the performance and maintaining the stability of real-time hybrid simulation(RTHS).However,existing methods have limitations in obtaining this local assessment in either the time domain or frequency domain.In this study,the instantaneous frequency is introduced to determine local control parameters for actuator tracking assessment in a real-time hybrid simulation.Instantaneous properties,including amplitude,delay,frequency and phase,are then calculated based on analytic signals translated from actuator tracking signals through the Hilbert transform.Potential issues are discussed and solutions are proposed for calculation of local control parameters.Numerical simulations are first conducted for sinusoidal and chirp signals with time varying amplitude error and delay to demonstrate the potential of the proposed method.Laboratory tests also are conducted for a predefined random signal as well as the RTHS of a single degree of freedom structure with a self-centering viscous damper to experimentally verify the effectiveness of the proposed use of the instantaneous frequency.Results from the ensuing analysis clearly demonstrate that the instantaneous frequency provides great potential for local control assessment,and the proposed method enables local tracking parameters with good accuracy.

Models to Simulate Effective Coverage of Fire Station Based on Real-Time Travel Times

In recent years,frequent fire disasters have led to enormous damage in China.Effective firefighting rescues can minimize the losses caused by fires.During the rescue processes,the travel time of fire trucks can be severely affected by traffic conditions,changing the effective coverage of fire stations.However,it is still challenging to determine the effective coverage of fire stations considering dynamic traffic conditions.This paper addresses this issue by combining the traveling time calculationmodelwith the effective coverage simulationmodel.In addition,it proposes a new index of total effective coverage area(TECA)based on the time-weighted average of the effective coverage area(ECA)to evaluate the urban fire services.It also selects China as the case study to validate the feasibility of the models,a fire station(FS-JX)in Changsha.FS-JX station and its surrounding 9,117 fire risk points are selected as the fire service supply and demand points,respectively.A total of 196 simulation scenarios throughout a consecutiveweek are analyzed.Eventually,1,933,815 sets of valid sample data are obtained.The results showed that the TECA of FS-JX is 3.27 km^(2),which is far below the standard requirement of 7.00 km^(2) due to the traffic conditions.The visualization results showed that three rivers around FS-JX interrupt the continuity of its effective coverage.The proposed method can provide data support to optimize the locations of fire stations by accurately and dynamically determining the effective coverage of fire stations.

Real-Time Monitoring Method for Cow Rumination Behavior Based on Edge Computing and Improved MobileNet v3

[Objective]Real-time monitoring of cow ruminant behavior is of paramount importance for promptly obtaining relevant information about cow health and predicting cow diseases.Currently,various strategies have been proposed for monitoring cow ruminant behavior,including video surveillance,sound recognition,and sensor monitoring methods.How‐ever,the application of edge device gives rise to the issue of inadequate real-time performance.To reduce the volume of data transmission and cloud computing workload while achieving real-time monitoring of dairy cow rumination behavior,a real-time monitoring method was proposed for cow ruminant behavior based on edge computing.[Methods]Autono‐mously designed edge devices were utilized to collect and process six-axis acceleration signals from cows in real-time.Based on these six-axis data,two distinct strategies,federated edge intelligence and split edge intelligence,were investigat‐ed for the real-time recognition of cow ruminant behavior.Focused on the real-time recognition method for cow ruminant behavior leveraging federated edge intelligence,the CA-MobileNet v3 network was proposed by enhancing the MobileNet v3 network with a collaborative attention mechanism.Additionally,a federated edge intelligence model was designed uti‐lizing the CA-MobileNet v3 network and the FedAvg federated aggregation algorithm.In the study on split edge intelli‐gence,a split edge intelligence model named MobileNet-LSTM was designed by integrating the MobileNet v3 network with a fusion collaborative attention mechanism and the Bi-LSTM network.[Results and Discussions]Through compara‐tive experiments with MobileNet v3 and MobileNet-LSTM,the federated edge intelligence model based on CA-Mo‐bileNet v3 achieved an average Precision rate,Recall rate,F1-Score,Specificity,and Accuracy of 97.1%,97.9%,97.5%,98.3%,and 98.2%,respectively,yielding the best recognition performance.[Conclusions]It is provided a real-time and effective method for monitoring cow ruminant behavior,and the proposed federated edge intelligence model can be ap‐plied in practical settings.

Real-time hybrid simulation of structures equipped with viscoelastic-plastic dampers using a user-programmable computational platform

A user-programmable computational/control platform was developed at the University of Toronto that offers real-time hybrid simulation （RTHS） capabilities. The platform was verified previously using several linear physical substructures. The study presented in this paper is focused on further validating the RTHS platform using a nonlinear viscoelastic-plastic damper that has displacement, frequency and temperature-dependent properties. The validation study includes damper component characterization tests, as well as RTHS of a series of single-degree-of-freedom （SDOF） systems equipped with viscoelastic-plastic dampers that represent different structural designs. From the component characterization tests, it was found that for a wide range of excitation frequencies and friction slip loads, the tracking errors are comparable to the errors in RTHS of linear spring systems. The hybrid SDOF results are compared to an independently validated thermal- mechanical viscoelastic model to further validate the ability for the platform to test nonlinear systems. After the validation, as an application study, nonlinear SDOF hybrid tests were used to develop performance spectra to predict the response of structures equipped with damping systems that are more challenging to model analytically. The use of the experimental performance spectra is illustrated by comparing the predicted response to the hybrid test response of 2DOF systems equipped with viscoelastic-plastic dampers.

Real-Time Hybrid Simulation of Seismically Isolated Structures with Full-Scale Bearings and Large Computational Models

Hybrid simulation can be a cost effective approach for dynamic testing of structural components at full scale while capturing the system level response through interactions with a numerical model.The dynamic response of a seismically isolated structure depends on the combined characteristics of the ground motion,bearings,and superstructure.Therefore,dynamic full-scale system level tests of isolated structures under realistic dynamic loading conditions are desirable towards a holistic validation of this earthquake protection strategy.Moreover,bearing properties and their ultimate behavior have been shown to be highly dependent on rate-of-loading and scale size effects,especially under extreme loading conditions.Few laboratory facilities can test full-scale seismic isolation bearings under prescribed displacement and/or loading protocols.The adaptation of a full-scale bearing test machine for the implementation of real-time hybrid simulation is presented here with a focus on the challenges encountered in attaining reliable simulation results for large scale dynamic tests.These advanced real-time hybrid simulations of large and complex hybrid models with several thousands of degrees of freedom are some of the first to use high performance parallel computing to rapidly execute the numerical analyses.Challenges in the experimental setup included measured forces contaminated by delay and other systematic control errors in applying desired displacements.Friction and inertial forces generated by the large-scale loading apparatus can affect the accuracy of measured force feedbacks.Reliable results from real-time hybrid simulation requires implementation of compensation algorithms and correction of these various sources of errors.Overall,this research program confirms that real-time hybrid simulation is a viable testing method to experimentally assess the behavior of full-scale isolators while capturing interactions with the numerical models of the superstructure to evaluate system level and in-structure response.

Data-based real-time petrochemical gas diffusion simulation approach on virtual reality

Background Petrochemical products possess a high risk of flammability,explosivity,and toxicity,making petrochemical accidents exceedingly destructive.Therefore,disaster analysis,prediction,and real-time simulations have become important means of controlling and reducing accident hazards.Methods This study proposes a complete real-time simulation solution of gas diffusion with coordinate and concentration data,which was mainly aimed at simulating the types of harmful gas leakage and diffusion accidents in the petrochemical industry.The rendering effect was more continuous and accurate through grid homogenization and trilinear interpolation.This study presents a data processing and rendering parallelization process to enhance simulation efficiency.Gas concentration and fragment transparency were combined to synthesize transparent pixels in a scene.To ensure the approximate accuracy of the rendering effect,improve the efficiency of real-time rendering,and meet the requirement of intuitive perception using concentration data,a weighted blended order-independent transparency(OIT)with enhanced alpha weight is presented,which can provide a more intuitive perception of the hierarchical information of concentration data while preserving depth information.This study compares and analyzes three OIT algorithms-depth peeling,weighted blended OIT,and weighted blended OIT with enhanced alpha weight-in terms of rendering image quality,rendering time,required memory,and hierarchical information.Results Using weighted blended OIT with an enhanced alpha weight technique,the rendering time was shortened by 53.2%compared with that of the depth peeling algorithm,and the texture memory required was significantly smaller than that of the depth peeling algorithm.The rendering results of weighted blended OIT with an enhanced alpha weight were approximately accurate compared with those of the depth peeling algorithm as the ground truth,and there was no popping when surfaces passed through one another.Simultaneously,compared with weighted blended OIT,weighted blended OIT with an enhanced alpha weight achieved an intuitive perception of the hierarchical information of concentration data.

From the perspective of experimental practice: High-throughput computational screening in photocatalysis

Photocatalysis,a critical strategy for harvesting sunlight to address energy demand and environmental concerns,is underpinned by the discovery of high-performance photocatalysts,thereby how to design photocatalysts is now generating widespread interest in boosting the conversion effi-ciency of solar energy.In the past decade,computational technologies and theoretical simulations have led to a major leap in the development of high-throughput computational screening strategies for novel high-efficiency photocatalysts.In this viewpoint,we started with introducing the challenges of photocatalysis from the view of experimental practice,especially the inefficiency of the traditional“trial and error”method.Sub-sequently,a cross-sectional comparison between experimental and high-throughput computational screening for photocatalysis is presented and discussed in detail.On the basis of the current experimental progress in photocatalysis,we also exemplified the various challenges associated with high-throughput computational screening strategies.Finally,we offered a preferred high-throughput computational screening procedure for pho-tocatalysts from an experimental practice perspective(model construction and screening,standardized experiments,assessment and revision),with the aim of a better correlation of high-throughput simulations and experimental practices,motivating to search for better descriptors.

A deep reinforcement learning approach to gasoline blending real-time optimization under uncertainty

The gasoline inline blending process has widely used real-time optimization techniques to achieve optimization objectives,such as minimizing the cost of production.However,the effectiveness of real-time optimization in gasoline blending relies on accurate blending models and is challenged by stochastic disturbances.Thus,we propose a real-time optimization algorithm based on the soft actor-critic(SAC)deep reinforcement learning strategy to optimize gasoline blending without relying on a single blending model and to be robust against disturbances.Our approach constructs the environment using nonlinear blending models and feedstocks with disturbances.The algorithm incorporates the Lagrange multiplier and path constraints in reward design to manage sparse product constraints.Carefully abstracted states facilitate algorithm convergence,and the normalized action vector in each optimization period allows the agent to generalize to some extent across different target production scenarios.Through these well-designed components,the algorithm based on the SAC outperforms real-time optimization methods based on either nonlinear or linear programming.It even demonstrates comparable performance with the time-horizon based real-time optimization method,which requires knowledge of uncertainty models,confirming its capability to handle uncertainty without accurate models.Our simulation illustrates a promising approach to free real-time optimization of the gasoline blending process from uncertainty models that are difficult to acquire in practice.

Distributed Computation Models for Data Fusion System Simulation

An attempt has been made to develop a distributed software infrastructure model for onboard data fusion system simulation, which is also applied to netted radar systems, onboard distributed detection systems and advanced C3I systems. Two architectures are provided and verified: one is based on pure TCP/IP protocol and C/S model, and implemented with Winsock, the other is based on CORBA (common object request broker architecture). The performance of data fusion simulation system, i.e. reliability, flexibility and scalability, is improved and enhanced by two models. The study of them makes valuable explore on incorporating the distributed computation concepts into radar system simulation techniques.

Three-dimensional finite element simulation and reconstruction of jointed rock models using CT scanning and photogrammetry

The geometry of joints has a significant influence on the mechanical properties of rocks.To simplify the curved joint shapes in rocks,the joint shape is usually treated as straight lines or planes in most laboratory experiments and numerical simulations.In this study,the computerized tomography (CT) scanning and photogrammetry were employed to obtain the internal and surface joint structures of a limestone sample,respectively.To describe the joint geometry,the edge detection algorithms and a three-dimensional (3D) matrix mapping method were applied to reconstruct CT-based and photogrammetry-based jointed rock models.For comparison tests,the numerical uniaxial compression tests were conducted on an intact rock sample and a sample with a joint simplified to a plane using the parallel computing method.The results indicate that the mechanical characteristics and failure process of jointed rocks are significantly affected by the geometry of joints.The presence of joints reduces the uniaxial compressive strength (UCS),elastic modulus,and released acoustic emission (AE) energy of rocks by 37%–67%,21%–24%,and 52%–90%,respectively.Compared to the simplified joint sample,the proposed photogrammetry-based numerical model makes the most of the limited geometry information of joints.The UCS,accumulative released AE energy,and elastic modulus of the photogrammetry-based sample were found to be very close to those of the CT-based sample.The UCS value of the simplified joint sample (i.e.38.5 MPa) is much lower than that of the CT-based sample (i.e.72.3 MPa).Additionally,the accumulative released AE energy observed in the simplified joint sample is 3.899 times lower than that observed in the CT-based sample.CT scanning provides a reliable means to visualize the joints in rocks,which can be used to verify the reliability of photogrammetry techniques.The application of the photogrammetry-based sample enables detailed analysis for estimating the mechanical properties of jointed rocks.

Desulfurization characteristics of slaked lime and regulation optimization of circulating fluidized bed flue gas desulfurization process--A combined experimental and numerical simulation study

Circulating fluidized bed flue gas desulfurization(CFB-FGD) process has been widely applied in recent years. However, high cost caused by the use of high-quality slaked lime and difficult operation due to the complex flow field are two issues which have received great attention. Accordingly, a laboratory-scale fluidized bed reactor was constructed to investigate the effects of physical properties and external conditions on desulfurization performance of slaked lime, and the conclusions were tried out in an industrial-scale CFB-FGD tower. After that, a numerical model of the tower was established based on computational particle fluid dynamics(CPFD) and two-film theory. After comparison and validation with actual operation data, the effects of operating parameters on gas-solid distribution and desulfurization characteristics were investigated. The results of experiments and industrial trials showed that the use of slaked lime with a calcium hydroxide content of approximately 80% and particle size greater than 40 μm could significantly reduce the cost of desulfurizer. Simulation results showed that the flow field in the desulfurization tower was skewed under the influence of circulating ash. We obtained optimal operating conditions of 7.5 kg·s^(-1)for the atomized water flow, 70 kg·s^(-1)for circulating ash flow, and 0.56 kg·s^(-1)for slaked lime flow, with desulfurization efficiency reaching 98.19% and the exit flue gas meeting the ultraclean emission and safety requirements. All parameters selected in the simulation were based on engineering examples and had certain application reference significance.

Real-Time Wind Speed Analysis at Wind-Damaged Tower of a Transmission Line

Affected by the Super Typhoon“Mangkhut,”a total of five base towers of a transmission line in the mountainous area of China collapsed.In this paper,a mathematical model is established based on the Shuttle Radar Topography Mission(SRTM)data near the accident tower.The measured wind speed in the plain area under the mountain is used as the calculation boundary condition.The wind speed at the top of the mountain is calculated by using a numerical simulation method.The design wind speed and calculated wind speed at the tower site are compared,and the influence of wind speed on tower position in this wind disaster accident is analyzed.

Recent Advances in Computational Simulation of Macro-,Meso-,and Micro-Scale Biomimetics Related Fluid Flow Problems

Over the last decade, computational methods have been intensively applied to a variety of scientific researches and engineering designs. Although the computational fluid dynamics （CFD） method has played a dominant role in studying and simulating transport phenomena involving fluid flow and heat and mass transfers, in recent years, other numerical methods for the simulations at meso- and micro-scales have also been actively applied to solve the physics of complex flow and fluid-interface interactions. This paper presents a review of recent advances in multi-scale computational simulation of biomimetics related fluid flow problems. The state-of-the-art numerical techniques, such as lattice Boltzmann method （LBM）, molecular dynamics （MD）, and conventional CFD, applied to different problems such as fish flow, electro-osmosis effect of earthworm motion, and self-cleaning hydrophobic surface, and the numerical approaches are introduced. The new challenging of modelling biomimetics problems in developing the physical conditions of self-clean hydrophobic surfaces is discussed.

FEM model for real-time guide wire simulation in vasculature

A model suitable for describing the mechanical response of thin elastic objects is proposed to simulate the deformation of guide wires in minimally invasive interventions. The main objective of this simulation is to provide doctors an opportunity to rehearse the surgery and select an optimal operation plan before the real surgery. In this model the guide wire is discretized with the multi-body representation and its elastic energy derivate from elastic theory is a polynomial function of the nodal displacements. The vascular structure is represented by a tetrahedron mesh extended from the triangular mesh of the artery, which can be extracted from the patient＇s CT image data. The model applies the energy decline process of the conjugate gradient method to the deformation simulation of the guide wire. Experimental results show that the polynomial relationship between elastic energy and nodal displacements tremendously simplifies the evaluation of the conjugate gradient method and significantly improves the model＇s efficiency. Compared with models depending on an explicit scheme for evaluation, the new model is not only non-conditionally stable but also more efficient. The model can be applied to the real-time simulation of guide wire in a vascular structure.

Simulation and Analysis on the Two-Phase Flow Fields in a Rotating-Stream-Tray Absorber by Using Computational Fluid Dynamics

The flow field of gas and liquid in a φ150mm rotating-stream-tray (RST) scrubber is simulated by using computational fluid dynamic (CFD) method. The sismulation is based on the two-equation RNG κ-ε turbulence model, Eulerian multiphase model, and a real-shape 3D model with a huge number of meshes. The simulation results include detailed information about velocity, pressure, volume fraction and so on. Some features of the flow field are obtained: liquid is atomized in a thin annular zone; a high velocity air zone prevents water drops at the bottom from flying towards the wall; the pressure varies sharply at the end of blades and so on. The results will be helpful for structure optimization and engineering design.

COMPUTATIONAL FLUID DYNAMICS(CFD) SIMULATIONS OF DRAG REDUCTION WITH PERIODIC MICRO-STRUCTURED WALL

Computational fluid dynamics（CFD） simulations are adopted to investigate rectangular microchannel flows with various periodic micro-structured wall by introducing velocity slip boundary condition at low Reynolds number. The purpose of the current study is to numerically find out the effects of periodic micro-structured wall on the flow resistance in rectangular microchannel with the different spacings between microridges ranging from 15 to 60 pm. The simulative results indicate that pressure drop with different spacing between microridges increases linearly with flow velocity and decreases monotonically with slip velocity; Pressure drop reduction also increases with the spacing between microridges at the same condition of slip velocity and flow velocity. The results of numerical simulation are compared with theoretical predictions and experimental results in the literatures. It is found that there is qualitative agreement between them.

On modeling approach for embedded real-time software simulation testing

Modeling technology has been introduced into software testing field. However, how to carry through the testing modeling effectively is still a difficulty. Based on combination of simulation modeling technology and embedded real-time software testing method, the process of simulation testing modeling is studied first. And then, the supporting environment of simulation testing modeling is put forward. Furthermore, an approach of embedded real-time software simulation testing modeling including modeling of cross-linked equipments of system under testing （SUT）, test case, testing scheduling, and testing system service is brought forward. Finally, the formalized description and execution system of testing models are given, with which we can realize real-time, closed loop, mad automated system testing for embedded real-time software.

Computational Mass Transfer Method for Chemical Process Simulation

The recent works on the development of computational mass transfer （CMT） method and its applications in chemical process simulation are reviewed. Some development strategies and challenges in future research are also discussed.

Simulation of large-scale numerical substructure in real-time dynamic hybrid testing

A solution scheme is proposed in this paper for an existing RTDHT system to simulate large-scale finite element （FE） numerical substructures. The analysis of the FE numerical substructure is split into response analysis and signal generation tasks, and executed in two different target computers in real-time. One target computer implements the response analysis task, wherein a large time-step is used to solve the FE substructure, and another target computer implements the signal generation task, wherein an interpolation program is used to generate control signals in a small time-step to meet the input demand of the controller. By using this strategy, the scale of the FE numerical substructure simulation may be increased significantly. The proposed scheme is initially verified by two FE numerical substructure models with 98 and 1240 degrees of freedom （DOFs）. Thereafter, RTDHTs of a single frame-foundation structure are implemented where the foundation, considered as the numerical substructure, is simulated by the FE model with 1240 DOFs. Good agreements between the results of the RTDHT and those from the FE analysis in ABAQUS are obtained.