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.

Effect of the Particle Packing Configuration on Fixed Bed Performance

Fixed-bed reactors are generally considered the optimal choice for numerous multi-phase catalytic reactions due to their excellent performance and stability.However,conventional fixed beds often encounter challenges related to inadequate mass transfer and a high pressure drop caused by the non-uniform void fraction distribution.To enhance the overall performance of fixed beds,the impact of different packing configurations on performance was investigated.Experimental and simulation methods were used to investigate the fluid flow and mass transfer performances of various packed beds under different flow rates.It was found that structured beds exhibited a significantly lower pressure drop per unit length than conventional packed beds.Furthermore,the packing configurations had a critical role in improving the overall performance of fixed beds.Specifically,structured packed beds,particularly the H-2 packing configuration,effectively reduced the pressure drop per unit length and improved the mass transfer efficiency.The H-2 packing configuration consisted of two parallel strips of particles in each layer,with strips arranged perpendicularly between adjacent layers,and the spacing between the strips varied from layer to layer.

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.

Effects of sand-fixing and windbreak forests on wind flow:a synthesis of results from field experiments and numerical simulations

Sand-fixing and windbreak forests are widely used to protect or/and improve the ecological environments in arid and semi-arid regions. A full understanding of wind flow characteristics is essential to arranging the patterns of these protective forests for enhancing the effectiveness. In this study, the wind velocity over the underlying surface with sand-fixing forests and windbreak forests at the heights of 1–49 m was monitored from two 50-m high observation towers in an oasis of Minqin, Gansu Province of China. The wind velocities were simulated at different locations over these protective forests between those two towers by a two-dimensional Computational Fluid Dynamics（CFD） model. The results showed that at the heights of 1–49 m, the wind velocity profiles followed a classical logarithm law at the edge of the oasis and a multilayer structure inside the oasis. With increasing number of sand-fixing forest and windbreak forest arrays, the wind velocity at the heights of 1–49 m generally decreased along the downstream direction of the prevailing wind. Specifically, below the height of windbreak forests, the wind velocity decelerates as the airflow approaches to the windbreak forests and then accelerates as the airflow passes over the windbreak forests. In contrast, above the height of windbreak forests, the wind velocity accelerates as the airflow approaches to the windbreak forests and then generally decelerates as the airflow passes over the windbreak forests. Both the array number and array spacing of sand-fixing and windbreak forests could influence the wind velocity. The wind protection effects of sand-fixing forests were closely related to the array spacing of windbreak forests and increased with the addition of sand-fixing forests when the array of the forests was adequately spaced. However, if the array spacing of windbreak forests was smaller than seven times of the heights of windbreak forests, the effects were reduced or completely masked by the effects of windbreak forests. The results could offer theoretical guidelines on how to systematically arrange the patterns of sand-fixing and windbreak forests for preventing wind erosion in the most convenient and the cheapest ways.

Effects of different numerical algorithms on simulation of chemical dissolution-front instability in fluid-saturated porous rocks

Many scientific and engineering problems need to use numerical methods and algorithms to obtain computational simulation results because analytical solutions are seldom available for them.The chemical dissolution-front instability problem in fluid-saturated porous rocks is no exception.Since this kind of instability problem has both the conventional(i.e.trivial)and the unconventional(i.e.nontrivial)solutions,it is necessary to examine the effects of different numerical algorithms,which are used to solve chemical dissolution-front instability problems in fluid-saturated porous rocks.Toward this goal,two different numerical algorithms associated with the commonly-used finite element method are considered in this paper.In the first numerical algorithm,the porosity,pore-fluid pressure and acid/solute concentration are selected as basic variables,while in the second numerical algorithm,the porosity,velocity of pore-fluid flow and acid/solute concentration are selected as basic variables.The particular attention is paid to the effects of these two numerical algorithms on the computational simulation results of unstable chemical dissolution-front propagation in fluid-saturated porous rocks.The related computational simulation results have demonstrated that:1)the first numerical algorithm associated with the porosity-pressure-concentration approach can realistically simulate the evolution processes of unstable chemical dissolution-front propagation in chemical dissolution systems.2)The second numerical algorithm associated with the porosity-velocity-concentration approach fails to simulate the evolution processes of unstable chemical dissolution-front propagation.3)The extra differential operation is the main source to result in the failure of the second numerical algorithm.

Sheltering effect of punched steel plate sand fences for controlling blown sand hazards along the Golmud-Korla Railway:Field observation and numerical simulation studies

Sand fences made of punched steel plate(PSP)have recently been applied to control wind-blown sand in desertified and Gobi areas due to their strong wind resistance and convenient in situ construction.However,few studies have assessed the protective effect of PSP sand fences,especially through field observations.This study analyzes the effects of double-row PSP sand fences on wind and sand resistance using field observations and a computational fluid dynamics(CFD)numerical simulation.The results of field observations showed that the average windproof efficiencies of the first-row and second-row sand fences were 79.8%and 70.8%,respectively.Moreover,the average windproof efficiencies of the numerical simulation behind the first-row and second-row sand fences were 89.8%and 81.1%,respectively.The sand-resistance efficiency of the double-row PSP sand fences was 65.4%.Sand deposition occurred close to the first-row sand fence;however,there was relatively little sand on the leeward side of the second-row sand fence.The length of sand accumulation near PSP sand fences obtained by numerical simulation was basically consistent with that through field observations,indicating that field observations combined with numerical simulation can provide insight into the complex wind-blown sand field over PSP sand fences.This study indicates that the protection efficiency of the double-row PSP sand fences is sufficient for effective control of sand hazards associated with extremely strong wind in the Gobi areas.The output of this work is expected to improve the future application of PSP sand fences.

CFD Simulation and Experimental Study of a New Elastic Blade Wave Energy Converter

Small moving vehicles represent an important category of marine engineering tools and devices(equipment)typically used for ocean resource detection and maintenance of marine rights and interests.The lack of efficient power supply modes is one of the technical bottlenecks restricting the effective utilisation of this type of equipment.In this work,the performance characteristics of a new type of elastic-blade/wave-energy converter(EBWEC)and its core energy conversion component(named wave energy absorber)are comprehensively studied.In particular,computational fluid dynamics(CFD)simulations and experiments have been used to analyze the hydrodynamics and performance characteristics of the EBWEC.The pressure cloud diagrams relating to the surface of the elastic blade were obtained through two-way fluid-solid coupling simulations.The influence of blade thickness and relative speed on the performance characteristics of EBWEC was analyzed accordingly.A prototype of the EBWEC and its bucket test platform were also developed.The power characteristics of the EBWEC were analyzed and studied by using the blade thickness and motion cycle as control variables.The present research shows that the EBWEC can effectively overcome the performance disadvantages related to the transmission shaft torque load and power curve fluctuations of rigid blade wave energy converters(RBWEC).

Efficiency analysis of numerical integrations for finite element substructure in real-time hybrid simulation

Finite element（FE） is a powerful tool and has been applied by investigators to real-time hybrid simulations（RTHSs）. This study focuses on the computational efficiency, including the computational time and accuracy, of numerical integrations in solving FE numerical substructure in RTHSs. First, sparse matrix storage schemes are adopted to decrease the computational time of FE numerical substructure. In this way, the task execution time（TET） decreases such that the scale of the numerical substructure model increases. Subsequently, several commonly used explicit numerical integration algorithms, including the central difference method（CDM）, the Newmark explicit method, the Chang method and the Gui-λ method, are comprehensively compared to evaluate their computational time in solving FE numerical substructure. CDM is better than the other explicit integration algorithms when the damping matrix is diagonal, while the Gui-λ（λ = 4） method is advantageous when the damping matrix is non-diagonal. Finally, the effect of time delay on the computational accuracy of RTHSs is investigated by simulating structure-foundation systems. Simulation results show that the influences of time delay on the displacement response become obvious with the mass ratio increasing, and delay compensation methods may reduce the relative error of the displacement peak value to less than 5% even under the large time-step and large time delay.

Computational simulation of convective flow in the Earth crust under consideration of dynamic crust-mantle interactions

The finite element method was used to solve fluid dynamic interaction problems between the crust and mantle of the Earth. To consider different mechanical behaviours, the lithosphere consisting of the crust and upper mantle was simulated as fluid-saturated porous rocks, while the upper aesthenospheric part of the mantle was simulated as viscous fluids. Since the whole lithosphere was computationally simulated, the dynamic interaction between the crust and the upper mantle was appropriately considered. In particular, the mixing of mantle fluids and crustal fluids was simulated in the corresponding computational model. The related computational simulation results from an example problem demonstrate that the mantle fluids can flow into the crust and mix with the crustal fluids due to the resulting convective flows in the crust-mantle system. Likewise, the crustal fluids can also flow into the upper mantle and mix with the mantle fluids. This kind of fluids mixing and exchange is very important to the better understanding of the governing processes that control the ore body formation and mineralization in the upper crust of the Earth.

Computational fluid dynamics simulation of formaldehyde emission characteristics and its experimental validation in environment chamber

We investigated the effect of supply air rate and temperature on formaldehyde emission characteristics in an environment chamber.A three-dimensional computational fluid dynamics(CFD) chamber model for simulating formaldehyde emission in twelve different cases was developed for obtaining formaldehyde concentration by the area-weighted average method.Laboratory experiments were conducted in an environment chamber to validate the simulation results of twelve different cases and the formaldehyde concentration was measured by continuous sampling.The results show that there was good agreement between the model prediction and the experimental values within 4.3 difference for each case.The CFD simulation results varied in the range from 0.21 mg/m3 to 0.94 mg/m3,and the measuring results in the range from 0.17 mg/m3 to 0.87 mg/m3.The variation trend of formaldehyde concentration with supply air rate and temperature variation for CFD simulation and experiment measuring was consistent.With the existence of steady formaldehyde emission sources,formaldehyde concentration generally increased with the increase of temperature,and it decreased with the increase of air supply rate.We also provided some reasonable suggestions to reduce formaldehyde concentration and to improve indoor air quality for newly decorated rooms.

Computational fluid dynamics simulation of gas-liquid two phases flow in 320 m^3 air-blowing mechanical flotation cell using different turbulence models

According to the recently developed single-trough floating machine with the world's largest volume(inflatable mechanical agitation flotation machine with volume of 320 m3) in China, the gas-fluid two-phase flow in flotation cell was simulated using computational fluid dynamics method. It is shown that hexahedral mesh scheme is more suitable for the complex structure of the flotation cell than tetrahedral mesh scheme, and a mesh quality ranging from 0.7 to 1.0 is obtained. Comparative studies of the standard k-ε, k-ω and realizable k-ε turbulence models were carried out. It is indicated that the standard k-ε turbulence model could give a result relatively close to the practice and the liquid phase flow field is well characterized. In addition, two obvious recirculation zones are formed in the mixing zones, and the pressure on the rotor and stator is well characterized. Furthermore, the simulation results using improved standard k-ε turbulence model show that surface tension coefficient of 0.072, drag model of Grace and coefficient of 4, and lift coefficient of 0.001 can be achieved. The research results suggest that gas-fluid two-phase flow in large flotation cell can be well simulated using computational fluid dynamics method.

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.

Numerical simulation of stirred tanks using a hybrid immersed-boundary method

Conventionally, multiple reference frame(MRF) method and sliding mesh(SM) method are used in the simulation of stirred tanks, however, both methods have limitations. In this study, a hybrid immersed-boundary(IB)technique is developed in a finite difference context for the numerical simulation of stirred tanks. IBs based on Lagrangian markers and solid volume fractions are used for moving and stationary boundaries, respectively, to achieve optimal efficiency and accuracy. To cope with the high computational cost in the simulation of stirred tanks, the technique is implemented on computers with hybrid architecture where central processing units(CPUs) and graphics processing units(GPUs) are used together. The accuracy and efficiency of the present technique are first demonstrated in a relatively simple case, and then the technique is applied to the simulation of turbulent flow in a Rushton stirred tank with large eddy simulation(LES). Finally the proposed methodology is coupled with discrete element method(DEM) to accomplish particle-resolved simulation of solid suspensions in small stirred tanks. It demonstrates that the proposed methodology is a promising tool in simulating turbulent flow in stirred tanks with complex geometries.

Applying multi-scale simulations to materials research of nuclear fuels:A review

Computational simulation is an important technical means in research of nuclear fuel materials.Since nuclear fuel issues are inherently multi-scopic,it is imperative to study them with multi-scale simulation scheme.At present,the development of multi-scale simulation for nuclear fuel materials calls for a more systematic approach,in which lies the main purpose of this article.The most important thing in multi-scale simulation is to accurately formulate the goals to be achieved and the types of methods to be used.In this regard,we first summarize the basic principles and applicability of the simulation methods which are commonly used in nuclear fuel research and are based on different scales ranging from micro to macro,i.e.First-Principles(FP),Molecular Dynamics(MD),Kinetic Monte Carlo(KMC),Phase Field(PF),Rate Theory(RT),and Finite Element Method(FEM).And then we discuss the major material issues in this field,also ranging from micro-scale to macro-scale and covering both pellets and claddings,with emphasis on what simulation method would be most suitable for solving each of the issues.Finally,we give our prospective analysis and understanding about the feasible ways of multi-scale integration and relevant handicaps and challenges.

Hierarchical Visual Analysis and Steering Framework for Astrophysical Simulations

A framework for accelerating modern long-running astrophysical simulations is presented, which is based on a hierarchical architecture where computational steering in the high-resolution run is performed under the guide of knowledge obtained in the gradually refined ensemble analyses. Several visualization schemes for facilitating ensemble management, error analysis, parameter grouping and tuning are also integrated owing to the pluggable modular design. The proposed approach is prototyped based on the Flash code, and it can be extended by introducing userdefined visualization for specific requirements. Two real-world simulations, i.e., stellar wind and supernova remnant, are carried out to verify the proposed approach.

Influence of site selection on natural ventilation in Chinese traditional folk house

The relationship between the site selection of a hilly terrain and the natural ventilation of the Dangdamen building complex,which is a traditional folk house,is revealed by a computational fluid dynamics（CFD）simulation.The wind press and speed distributions around the building in four cases with different weather conditions and topographies are simulated.The simulation results show that a hill can reduce the absolute values of the wind pressure at the windward and leeward sides of the building.The encouraging effect of the patio on the natural ventilation in a terrain with a hill is greater than that without a hill.The same situation occurs when comparing the patio effects between summer and winter.The wind speed around the building can be reduced by the hill as it is an obstacle and the degrees of the influence of the hill in summer and in winter are quite different because of different wind directions.The analysis results show that this kind of site selection,with the hill to the north,is a suitable way to settle the conflict of the natural ventilation requirements in summer and in winter under subtropical climate conditions,especially in houses with patios.

CFD-supported optimization of flow distribution in quench tank for heat treatment of A357 alloy large complicated components

The flow distribution in quench tank for heat treatment of A357 alloy large complicated components was simulated using FLUENT computational fluid dynamics（CFD） software.The flow velocity and the uniformity of flow field in two types of quench tanks（with or without agitation system） were calculated.The results show that the flow field in the quench tank without agitation system has not evident regularity.While as for the quench tank with agitation system,the flow fields in different parameters have certain regularity.The agitation tanks have a distinct advantage over the system without agitation.Proper process parameters were also obtained.Finally,the tank model established in this work was testified by an example from publication.This model with high accuracy is able to optimize the tank structures and can be helpful for industrial production and theoretical investigation in the fields of heat treatment of large complicated components.

Numerical study of pressure drop for a new fibrous media model

An open-source computational fluid dynamics（CFD）code named OpenFOAM is used to validate the flow field characteristics（flow patterns and pressure drop）around a single cylinder.Results show that OpenFOAM is suitable for simulating the low Reynolds number flow and Shaw＇s analytical expression is one of the solutions to Stokes＇ paradox.Experiments are performed on fibrous media and OpenFOAM simulation is carried out using the Tronville-Rivers two-dimensional random fiber model in terms of the characteristics of pressure drop.It is shown that the Kuwabara model predicts the pressure drop of fibrous filter media more accurately than the Happel model,and the experimental pressure drop is between simulated pressure drops with both non-slip and full-slip boundaries on fiber surfaces.

Research progress in interface modification and thermal conduction behavior of diamond/metal composites

Diamond/metal composites are widely used in aerospace and electronic packaging fields due to their outstanding high thermal conductivity and low expansion.However,the difference in chemical properties leads to interface incompatibility between diamond and metal,which has a considerable impact on the performance of the composites.To improve the interface compatibility between diamond and metal,it is necessary to modify the interface of composites.This paper reviews the experimental research on interface modification and the application of computational simulation in diamond/metal composites.Combining computational simulation with experimental methods is a promising way to promote diamond/metal composite interface modification research.