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.

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.

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 simulation of wave propagation problems in infinite domains

This paper deals with the computational simulation of both scalar wave and vector wave propagation problems in infinite domains. Due to its advantages in simulating complicated geometry and complex material properties, the finite element method is used to simulate the near field of a wave propagation problem involving an infinite domain. To avoid wave reflection and refraction at the common boundary between the near field and the far field of an infinite domain, we have to use some special treatments to this boundary. For a wave radiation problem, a wave absorbing boundary can be applied to the common boundary between the near field and the far field of an infinite domain, while for a wave scattering problem, the dynamic infinite element can be used to propagate the incident wave from the near field to the far field of the infinite domain. For the sake of illustrating how these two different approaches are used to simulate the effect of the far field, a mathematical expression for a wave absorbing boundary of high-order accuracy is derived from a two-dimensional scalar wave radiation problem in an infinite domain, while the detailed mathematical formulation of the dynamic infinite element is derived from a two-dimensional vector wave scattering problem in an infinite domain. Finally, the coupled method of finite elements and dynamic infinite elements is used to investigate the effects of topographical conditions on the free field motion along the surface of a canyon.

Index of microcirculatory resistance: state-of-the-art and potential applications in computational simulation of coronary artery disease

The dysfunction of coronary microcirculation is an important cause of coronary artery disease(CAD).The index of microcirculatory resistance(IMR)is a quantitative evaluation of coronary microcirculatory function,which provides a significant reference for the prediction,diagnosis,treatment,and prognosis of CAD.IMR also plays a key role in investigating the interaction between epicardial and microcirculatory dysfunctions,and is closely associated with coronary hemodynamic parameters such as flow rate,distal coronary pressure,and aortic pressure,which have been widely applied in computational studies of CAD.However,there is currently a lack of consensus across studies on the normal and pathological ranges of IMR.The relationships between IMR and coronary hemodynamic parameters have not been accurately quantified,which limits the application of IMR in computational CAD studies.In this paper,we discuss the research gaps between IMR and its potential applications in the computational simulation of CAD.Computational simulation based on the combination of IMR and other hemodynamic parameters is a promising technology to improve the diagnosis and guide clinical trials of CAD.

Computational Simulation and Electrochemically Deposited Molecularly Imprinted Polymer-coated Carbon Glass Electrode for Triclosan Detection

Triclosan,a kind of multi-purpose biocide,was widely used household cleaning and personal care products.The widespread use of triclosan has potential risk to the ecotype and human health due to its release into sediment,surface and ground water resources.A molecularly imprinted electrochemical sensor for triclosan detection in cosmetic emulsion was synthesized and characterized.In order to determine the suitable monomer and evaluate the template-monomer geometry as well as the interaction energy in the template-monomer prepolymerization mixture,a computational study was applied.We found that the complex formed by hybrid monomers(triclosan(o-phenylenediamine-co-resorcinol))had more hydrogen bonds and larger binding energy than that by single kind of monomers(triclosan(o-phenylenediamine)2 and triclosan(resorcinol)2).Therefore,hybrid monomers were used to synthesize the imprinted electrochemical sensor,which exhibits a high sensitivity and selectivity for triclosan sensing with the detection range 0~15 ng·mL-1 and detection limit 0.41 ng·mL-1.

Synthesis,biochemical evaluation and computational simulations of new cytochrome bc1 complex inhibitors based on N-(4-aryloxyphenyl)phthalimides

The cytochrome bc1complex(the bc1complex or complex Ⅲ) is an attractive target for the discovery of numerous pharmaceuticals and pesticides. In order to identify new lead structures for this target, a new series of molecules, N-(4-aryloxyphenyl)phthalimides, were designed and synthesized in a straightforward manner. Our design strategy was to introduce a 4-aryloxyphenyl group, a fragment which exhibited promising bc1complex-inhibiting properties, into the aryl group of the valuable N-arylphthalimide backbone. Afterward, the biochemical evaluation of the newly synthesized compounds was carried out,and the results implied that several compounds demonstrated good activities against succinatecytochrome reductase(SCR, a mixture of mitochondrial complex Ⅱ and the bc1complex). Further studies confirmed that 3e’, a representative compound in this paper, was identified as an inhibitor of the bc1complex. Furthermore, computational simulations were also performed to better understand binding of 3e’ to the enzyme complex, which indicated that 3e’ should bind to the Qosite of the bc1complex.Consequently, we harbor the idea that this paper can provide a solid platform for synthesis and discovery of other bc1complex inhibitors.

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 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.

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.

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.

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.

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.

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.

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.