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.

Three-Dimensional Printing Conformal Cooling with Structural Lattices for Plastic Injection Molding

The design of three-dimensional printing based conformal cooling channels(CCCs)in injection molding holds great significance.Compared to CCCs,conformal cooling(CC)cavity solutions show promise in delivering enhanced cooling performance for plastic products,although they have been underexplored.In this research,CC cavity is designed within the mold geometry,reinforced by body-centered cubic(BCC)lattice structures to enhance mechanical strength.Three distinct BCC lattice variations have been integrated into the CC cavity:the BCC structure,BCC with cubes,and BCC with pillars.The thermal performances of the BCC lattice-added CC cavity are assessed numerically after experimental validation.To provide feasible solutions from viewpoints of thermal performances,various BCC lattice structure thicknesses are analyzed in the range of 0.8–1.2mm.Thermal simulation outcomes reveal that thicker lattice structures enhance mechanical strength but simultaneously lead to an increase in cooling time.Upon examining all the proposed CC cavity solutions supported by BCC,the cooling times range from 2.2 to 4 s,resulting in a reduction of 38.6%to 66.1%when compared to conventional straightdrilled channels.In contrast to CCCs,CC cavities have the potential to decrease the maximum temperature nonuniformity from 8.5 to 6 K.Nevertheless,the presence of lattice structures in CC cavity solutions results in an elevated pressure drop,reaching 2.8MPa,whereas the results for CCCs remain below2.1MPa.

The Effect of Inlet Angle Structure of Concave and Convex Plate on Internal Flow Characteristics of Alkaline Electrolyzer

The structure of the concave-convex plates has proven to be crucial in optimizing the internal flow characteristics of the electrolyzer for hydrogen production.This paper investigates the impact of the gradual expansion angle of the inlet channel on the internal flow field of alkaline electrolyzers.The flow distribution characteristics of concave-convex plates with different inlet angle structures in the electrolytic cell is discussed.Besides,the system with internal heat source is studied.The results indicate that a moderate gradual expansion angle is beneficial for enhancing fluid uniformity.However,an excessively large gradual expansion angle may lead to adverse reflux phenomena,reducing the overall performance of the electrolytic cell.

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.

Replacement of annular domain with trapezoidal domain in computational modeling of nonaqueous-phase-liquid dissolution-front propagation problems

In order to simulate the instability phenomenon of a nonaqueous phase liquid(NAPL) dissolution front in a computational model, the intrinsic characteristic length is commonly used to determine the length scale at which the instability of the NAPL dissolution front can be initiated. This will require a huge number of finite elements if a whole NAPL dissolution system is simulated in the computational model. Even though modern supercomputers might be used to tackle this kind of NAPL dissolution problem, it can become prohibitive for commonly-used personal computers to do so. The main purpose of this work is to investigate whether or not the whole NAPL dissolution system of an annular domain can be replaced by a trapezoidal domain, so as to greatly reduce the requirements for computer efforts. The related simulation results have demonstrated that when the NAPL dissolution system under consideration is in a subcritical state, if the dissolution pattern around the entrance of an annulus domain is of interest, then a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.However, if the dissolution pattern away from the vicinity of the entrance of an annulus domain is of interest, then a trapezoidal domain can be used to replace an annular domain in the computational simulation of the NAPL dissolution system. When the NAPL dissolution system under consideration is in a supercritical state, a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.

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.

Computational Fluid Dynamics Analysis of the Aortic Coarctation

In this work, we first investigated the hemodynamic parameters in the case of a normal aortic arch anatomy and in the case of aortic coarctation anatomy, both generated by using CFX-ICEM-ANSYS simulations. Then, we compared these results with those obtained for a proposed model without and with aortic coarctation, while introducing a real tridimensional magnetic resonance imaging geometry in the simulation process. The conclusion is that our proposed model reproduces, with a high agreement, the real case obtained from imaging data.

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.

Effects of porosity heterogeneity on chemical dissolution-front instability in fluid-saturated rocks

Homogeneity and heterogeneity are two totally different concepts in nature.At the particle length scale,rocks exhibit strong heterogeneity in their constituents and porosities.When the heterogeneity of porosity obeys the random uniform distribution,both the mean value and the variance of porosities in the heterogeneous porosity field can be used to reflect the overall heterogeneous characteristics of the porosity field.The main purpose of this work is to investigate the effects of porosity heterogeneity on chemical dissolution front instability in fluid-saturated rocks by the computational simulation method.The related computational simulation results have demonstrated that:1) since the propagation speed of a chemical dissolution front is inversely proportional to the difference between the final porosity and the mean value of porosities in the initial porosity field,an increase in the extent of the porosity heterogeneity can cause an increase in the mean value of porosities in the initial porosity field and an increase in the propagation speed of the chemical dissolution front.2) An increase in the variance of porosities in the initial porosity field can cause an increase in the instability probability of the chemical dissolution front in the fluid-saturated rock.3) The greater the mean value of porosities in the initial porosity field,the quicker the irregular morphology of the chemical dissolution front changes in the supercritical chemical dissolution systems.This means that the irregular morphology of a chemical dissolution front grows quicker in a porosity field of heterogeneity than it does in that of homogeneity when the chemical dissolution system is at a supercritical stage.

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).