Molecular dynamics simulation of the flow mechanism of shear-thinning fluids in a microchannel

Shear-thinning fluids have been widely used in microfluidic systems,but their internal flow mechanism is still unclear.Therefore,in this paper,molecular dynamics simulations are used to study the laminar flow of shear-thinning fluid in a microchannel.We validated the feasibility of our simulation method by evaluating the mean square displacement and Reynolds number of the solution layers.The results show that the change rule of the fluid system's velocity profile and interaction energy can reflect the shear-thinning characteristics of the fluids.The velocity profile resembles a top-hat shape,intensifying as the fluid's power law index decreases.The interaction energy between the wall and the fluid decreases gradually with increasing velocity,and a high concentration of non-Newtonian fluid reaches a plateau sooner.Moreover,the velocity profile of the fluid is related to the molecule number density distribution and their values are inversely proportional.By analyzing the radial distribution function,we found that the hydrogen bonds between solute and water molecules weaken with the increase in velocity.This observation offers an explanation for the shear-thinning phenomenon of the non-Newtonian flow from a micro perspective.

Temperature effect on nanotwinned Ni under nanoindentation using molecular dynamic simulation

Temperature effect on atomic deformation of nanotwinned Ni (nt-Ni) under localized nanoindentation is investigated in comparison with nanocrystalline Ni (nc-Ni) through molecular simulation.The nt-Ni exhibits enhanced critical load and hardness compared to nc-Ni,where perfect,stair-rod and Shockley dislocations are activated at (111),(111) and (111) slip planes in nt-Ni compared to only SSockley dislocation nucleation at (111) and (111) slip planes of nc-Ni.The nt-Ni exhibits a less significant indentation size effect in comparison with nc-Ni due to the dislocation slips hindrance of the twin boundary.The atomic deformation associated with the indentation size effect is investigated during dislocation transmission.Different from the decreasing partial slips parallel to the indenter surface in nc-Ni with increasing temperature,the temperaturedependent atomic deformation of nt-Ni is closely related to the twin boundary:from the partial slips parallel to the twin boundary (~10 K),to increased confined layer slips and decreased twin migration(300 K–600 K),to decreased confined layer slips and increased dislocation interaction of dislocation pinning and dissociation (900 K–1200 K).Dislocation density and atomic structure types through quantitative analysis are implemented to further reveal the above-mentioned dislocation motion and atomic structure alteration.Our study is helpful for understanding the temperature-dependent plasticity of twin boundary in nanotwinned materials.

Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations

Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectile impacts is thoroughly investigated using full-atomic molecular dynamics(MD)simulations.The study results show that the porous structure and density are key factors determining the mechanical response of GA under impact loading.Specifically,the impact-induced penetration of the projectile leads to the collapse of the pore structure,causing stretching and subsequent rupture of covalent bonds in graphene sheets.Moreover,the effects of temperature on the mechanical performance of GA have been proven to be minimal,thereby highlighting the mechanical stability of GA over a wide range of temperatures.Finally,the energy absorption density(EAD)and energy absorption efficiency(EAE)metrics are adopted to assess the energy absorption capacity of GA during projectile penetration.The research findings of this work demonstrate the significant potential of GA for energy absorption applications.

Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation

Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is proposed by using molecular dynamics simulation,and the relationship between ion-to-ion interaction and salt solubility in a simulated seawater water-salt system is investigated.By analyzing the variation of distance and contact time between ions in an electrolyte solution,from both spatial and temporal perspectives,new parameters were proposed to describe the interaction between ions:interaction distance(ID),and interaction time ratio(ITR).The best correlation between characteristic time ratio and solubility was found for a molar ratio of salt-to-water of 10:100 with a correlation coefficient of 0.96.For the same salt,a positive correlation was found between CTR and the molar ratio of salt and water.For type 1-1,type 2-1,type 1-2,and type 2-2 salts,the correlation coefficients between CTR and solubility were 0.93,0.96,0.92,and 0.98 for a salt-to-water molar ratio of 10:100,respectively.The solubility of multiple salts was predicted by simulations and compared with experimental values,yielding an average relative deviation of 12.4%.The new ion-interaction parameters offer significant advantages in describing strongly correlated and strongly hydrated electrolyte solutions.

Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects

To investigate the effect of void defects on the shock response of hexanitrohexaazaisowurtzitane(CL-20)co-crystals,shock responses of CL-20 co-crystals with energetic materials ligands trinitrotoluene(TNT),1,3-dinitrobenzene(DNB),solvents ligands dimethyl carbonate(DMC) and gamma-butyrolactone(GBL)with void were simulated,using molecular dynamics method and reactive force field.It is found that the CL-20 co-crystals with void defects will form hot spots when impacted,significantly affecting the decomposition of molecules around the void.The degree of molecular fragmentation is relatively low under the reflection velocity of 2 km/s,and the main reactions are the formation of dimer and the shedding of nitro groups.The existence of voids reduces the safety of CL-20 co-crystals,which induced the sensitivity of energetic co-crystals CL-20/TNT and CL-20/DNB to increase more significantly.Detonation has occurred under the reflection velocity of 4 km/s,energetic co-crystals are easier to polymerize than solvent co-crystals,and are not obviously affected by voids.The results show that the energy of the wave decreases after sweeping over the void,which reduces the chemical reaction frequency downstream of the void and affects the detonation performance,especially the solvent co-crystals.

Exploring the molecular mechanism of action of curcumin for the treatment of diabetic retinopathy,using network pharmacology,molecular docking,and molecular dynamics simulation

Background:Based on network pharmacology and molecular docking,the present study investigated the mechanism of curcumin(CUR)in diabetic retinopathy treatment.Methods:Based on the DisGeNET,Swiss TargetPrediction,GeneCards,Online Mendelian Inheritance in Man,Gene Expression Omnibus,and Comparative Toxicogenomics Database,the intersection core targets of CUR and diabetic retinopathy were identified.The intersection target was imported into the STRING database to obtain the protein-protein interaction map.According to the Database for Annotation,Visualization and Integrated Discovery database,the intersected targets were enriched in Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes pathways.Then Cytoscape 3.9.1 is used to make the drug-target-disease-pathway network.The mechanism of CUR and diabetic retinopathy was further verified by molecular docking and molecular dynamics simulation.Results:There were 203 intersecting targets of CUR and diabetic retinopathy identified.1320 GO entries were enriched for GO functions,which were primarily involved in the composition of cells such as identical protein binding,protein binding,enzyme binding,etc.It was found that 175 pathways were enriched using Kyoto Encyclopedia of Genes and Genomes pathway enrichment methods,which were mainly included in the lipid and atherosclerosis,AGE-RAGE signaling pathway in diabetic complications,pathways in cancer,etc.In the molecular docking analysis,CUR was found to have a good ability to bind to the core targets of albumin,IL-1B,and IL-6.The binding of albumin to CUR was further verified by molecular dynamics simulation.Conclusion:As a result of this study,CUR may exert a role in the treatment of diabetic retinopathy through multi-target and multi-pathway regulation,which indicates a possible direction of future research.

Refinement of Adaptive Dynamical Simulation of Quantum Mechanical Double Slit Interference Phenomenon

We applied adaptive dynamics to double slit interference phenomenon using particle model and obtained partial successful results in our previous report. The patterns qualitatively corresponded well with experiments. Several properties such as concave single slit pattern and large influence of slight displacement of the emission position were different from the experimental results. In this study we tried other slit conditions and obtained consistent patterns with experiments. We do not claim that the adaptive dynamics is the principle of quantum mechanics, but the present results support the probability of adaptive dynamics as the candidate of the basis of quantum mechanics. We discuss the advantages of the adaptive dynamical view for foundations of quantum mechanics.

A Unique Modelling Strategy to Dynamically Simulate the Performance of a Lobe Pump for Industrial Applications

The performance of a newly designed tri-lobe industrial lobe pump of high capacity is simulated by using commercial CFD solver Ansys Fluent. A combination of user-defined-functions and meshing strategies is employed to capture the rotation of the lobes. The numerical model is validated by comparing the simulated results with the literature values. The processes of suction, displacement, compression and exhaust are accurately captured in the transient simulation. The fluid pressure value remains in the range of inlet pressure value till the processes of suction and displacement are over. The instantaneous process of compression is accurately captured in the simulation. The movement of a particular working chamber is traced along the gradual degree of lobe’s rotation. At five different degrees of lobe’s rotation, pressure contour plots are reported which clearly shows the pressure values inside the working chamber. Each pressure value inside the working chamber conforms to the particular process in which the working chamber is operating. Finally, the power requirement at the shaft of rotation is estimated from the simulated values. The estimated value of power requirement is 3.61 BHP FHP whereas the same calculated theoretically is 3 BHP FHP. The discrepancy is attributed to the assumption of symmetry of blower along the thickness.

Exploring the moderating role of financial development in environmental Kuznets curve for South Africa:fresh evidence from the novel dynamic ARDL simulations approach

The extant literature has produced mixed evidence on the relationship between finan-cial development and ecological sustainability.This work addresses this conundrum by investigating financial development’s direct and indirect consequences on ecologi-cal quality utilizing the environmental Kuznets curve(EKC)methodological approach.Our empirical analysis is based on the novel dynamic autoregressive distributed lag simulations approach for South Africa between 1960 and 2020.The results,which used five distinct financial development measures,demonstrate that financial develop-ment boosts ecological integrity and environmental sustainability over the long and short terms.In the instance of South Africa,we additionally confirm the validity of the EKC theory.More importantly,the outcomes of the indirect channels demonstrate that financial development increases energy usage’s role in causing pollution while attenuating the detrimental impacts of economic growth,trade openness,and foreign direct investment on ecological quality.Moreover,the presence of an inadequate financial system is a requirement for the basis of the pollution haven hypothesis(PHH),which we examine using trade openness and foreign direct investment variables.PHH for both of these variables disappears when financial development crosses specified thresholds.Finally,industrial value addition destroys ecological quality while tech-nological innovation enhances it.This research provides some crucial policy recom-mendations and fresh perspectives for South Africa as it develops national initiatives to support ecological sustainability and reach its net zero emissions goal.

In situ TEM observations and molecular dynamics simulations of deformation defect activities in Mg via nanoindentation

In this work, we performed in situ nanoindentation in TEM to capture the real-time dislocation and twinning activities in pure Mg during loading and unloading. We demonstrated that the screw component of dislocations glides continuously, while the edge components rapidly become sessile during loading. The twin tip propagation is intermittent, whereas the twin boundary migration is more continuous. During unloading, we observed the elastic strain relaxation causes both dislocation retraction and detwinning. Moreover,we note that the plastic zone comprised of dislocations in Mg is well-defined, which contrasts with the diffused plastic zones observed in face-centered cubic metals under the nanoindentation impressions. Additionally, molecular dynamics simulations were performed to study the formation and evolution of deformation-induced crystallographic defects at the early stages of indentation. We observed that,in addition to dislocations, the I1stacking fault bounded with a <1/2c+p> Frank loop can be generated from the plastic zone ahead of the indenter, and potentially serve as a nucleation source for abundant dislocations observed experimentally. These new findings are anticipated to provide new knowledge on the deformation mechanisms of Mg, which are difficult to obtain through conventional ex situ approaches. These observations may serve as a baseline for simulation work that investigate the dynamics of dislocation slip and twinning in Mg and alloys.

Understanding the interfacial behaviors of benzene alkylation with butene using chloroaluminate ionic liquid catalyst: A molecular dynamics simulation

To better understand the benzene alkylation with chloroaluminate ionic liquids(ILs) as catalyst, the interfacial properties between the benzene/butene binary reactants and chloroaluminate ILs with varying cation alkyl chain length and different anions were investigated using molecular dynamics(MD) simulations. The results indicate that ILs can obviously improve the interfacial width, solubility and diffusion of reactants compared to H_(2)SO_(4). The longer alkyl chains of cations present a density enrichment at the interface and protrude into the binary reactants phase. Furthermore, the ILs consisting of 1-octyl-3-methylimidazolium cations([Omim]^(+)) and the stronger acidity heptachlorodialuminate anions([Al_(2)Cl_(7)]^(-)) are more beneficial to promote the interfacial width and facilitate the dissolution and diffusion of benzene in both the IL bulk and the interfacial region in comparison to the ones with shorter alkyl chains cations and weaker acidity anions. The information gives us a better guideline for the design of ILs for benzene alkylation.

Dynamic phasor-based hybrid simulation for multi-inverter grid-connected system

To realize the efficient transient simulation of a grid-connected power generation system based on multiple inverters, this paper proposes a hybrid simulation method integrating the models of electromagnetic transient and dynamic phasors. Based on a demonstration of the concepts and properties of dynamic phasors, the models of single-phase and three-phase inverters described by dynamic phasors are established first. Considering the numerical compatibility problem between dynamic phasors and instantaneous values, an interface scheme between dynamic phasors and instantaneous values is designed, and the efficiency and precision differences of various transformation methods are compared in detail.Finally, by utilizing MATLAB/Simulink, a hybrid simulation platform of a multi-inverter grid-connected system is built, and the efficiency and accuracy of the hybrid simulation are validated via comparison with the full electromagnetic transient simulation.

Molecular Dynamics Simulation of Interface Properties between Water-Based Inorganic Zinc Silicate Coating Modified by Organosilicone and Iron Substrate

The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibrium state,equilibrium concentration distribution,MSD of layer and different groups,and interaction energy of two interface models,the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale.It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage(t<20 ps).It can be seen from the multiple peak states of concentration distribution that the iron substrate,organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment.The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating.The interface thickness decreased from 7.45 to 6.82Å,the MSD of free zinc powder was effectively reduced,and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.

Molecular Dynamics Simulation of Hydrate Decomposition Under Action of Alcohol Inhibitors

The molecular dynamics method is used to investigate decomposition of methane hydrate at different temperatures,pressures and concentrations of inhibitor.By analyzing the parameters of system conformation,mean square displacement and radial distribution function,the decomposition of hydrate in the presence of alcohol inhibitors ethylene glycol and glycerol is explored.The results show that the hydroxyl groups in alcohol molecules can destroy the cage structure of hydrate,and form hydrogen bonds with nearby water molecules to effectively prevent the reformation of hydrate.Therefore,ethylene glycol and glycerol serve as inhibitors of methane hydrate,furthermore,in terms of inhibition effect,glycerol is better than ethylene glycol by comparing rate of hydrate decomposition.

Dynamic Mechanical Behavior and Numerical Simulation of an Ancient Underground Rock Mass under Impact Loading

To study the dynamic mechanical properties of tuff under different environmental conditions,the tuff from an ancient quarry in Shepan Island was prepared.The impact damage to the rock was tested using a triaxial dynamic impact mechanical testing system(TDIMTS)with different ground stresses,temperatures,and groundwater pressures.The time-strain relationship,dynamic stress-strain relationship,energy dissipation law,energy-peak strain relationship,and the impact damage pattern of the tuff specimens under impact air pressures were investigated.The TDIMTS experiment on ancient underground rock mass under impact loading was also simulated using the finite element analysis software LS-DYNA based on the Holmquist-Johnson-Cook(HJC)material model.The dynamic failure process,failure pattern and peak stress of tuff specimen were calculated.The simulation results obtained using the above methods were in good agreement with the experimental results.The results of the dynamic experiment show that with the same local stress,groundwater pressure,and temperature,the damage to the tuff specimens caused by blasting and quarrying disturbances gradually increases as the impact pressure increases.Under the same local stress,groundwater pressure,and temperature,the energy required to rupture the tuffs in ancient underground caverns is relatively small if the impact pressure is low accordingly,but as the impact pressure increases,the damage to the tuff caused by quarrying disturbance gradually increases.The damage gradually increases and the degree of damage to the tuff and the strain energy exhibit asymptotic growth when the tuff specimens are subjected to the greater strain energy,increasing the degree of rupturing of the tuff.In addition,the average crushing size decreases with increasing strain energy.By comparing the simulation results with the experimental results,it was found that the HJC model reflected the dynamic impact performance of tuff specimen,and the simulation results showed an evident strain rate effect.These results of this study can offer some guidance and theoretical support for the stability evaluation,protection,and safe operation of the ancient underground caverns in future.

Simulation-based Graphic Method for Dynamic System Modeling

The first step for engineering students to understand the practical system is to describe the system,which means to establish the mathematic model for the considered system.However,traditional mathematical modeling techniques are not readily assimilated by students,because the traditional modeling needs to obey the complicated physical laws for different engineering areas and requires a highly iterative process.In this paper,the simulation-based graphic modeling method is introduced to help students model the system and improve their performance in engineering education.The results from the questionnaire indicate that the simulation-based graphic method can help students to do the modeling of the system and improve their performance compared to the traditional ways.

Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants

The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.

Elucidating the molecular targets of Curcuma longa for breast cancer treatment using network pharmacology,molecular docking and molecular dynamics simulation

Background:To elucidate the molecular mechanisms of Curcuma longa(C.longa)in breast cancer treatment.Methods:Phytocompounds of C.longa were obtained from Dr.Duke’s Phytochemical and Ethnobotanical Database.Potential active targets were retrieved from Bindingdb,SEA and Swiss Target Prediction databases.Breast cancer targets were retrieved from the Therapeutic Target Database.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were done using DAVID and KOBAS3.0 databases respectively.The Cytoscape software was used to construct the phytocompound-target-pathway network.The PyRx and Desmond software were utilized for molecular docking and molecular dynamics simulation respectively.Results:Out of one hundred and fifty-six phytocompounds,fifty-four modulated proteins involved in breast cancer.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated C.longa exerts its therapeutic effect through regulating several key pathways.Molecular docking analysis revealed that most phytocompounds of C.longa had a good affinity with the key targets.Molecular dynamics simulation showed that ethinylestradiol formed stable ligand-protein complexes.Conclusion:The results of this study will enhance our understanding of the potential molecular mechanisms by which C.longa inhibits breast cancer and lay a foundation for future experimental studies.

基于Plant Simulation的化纤自动落丝系统仿真实验分析

基于Plant Simulation软件,构建一种化纤自动落丝系统的3D数字化模型,对系统效率关键输入因子进行参数化设置,将系统各工位三维数字模型导入软件中建立层次化运动机构图形结构,并运用Simltalk语言实现三维动作仿真,通过基础物理参数设置,保证了仿真数字化模型与现实系统更具一致性。通过多级实验设计分析了系统影响因子对于系统效率的影响特性曲线,并进一步通过动态参数化实验方法,计算出双输入因子对系统效能影响的敏感度。该实验结果可为化纤自动落丝系统的建设成本控制与可行性分析提供指导,具有较好的工程应用价值。

Dynamic analysis of axle box bearings on the high-speed train caused by wheel-rail excitation

To explore the impact of wheel-rail excitation on the dynamic performance of axle box bearings,a dynamic model of the high-speed train including axle box bearings is developed.Subsequently,the dynamic response characteristics of the axle box bearing are examined.The investigation focuses on the acceleration characteristics of bearing vibration under excitation of track irregularities and wheel flats.In addition,experiments on both normal and faulty bearings are conducted separately,and the correctness of the model and some conclusions are verified.According to the research,track irregularity is unfavorable for bearing fault detection based on resonance demodulation.Under the same speed conditions,the acceleration peak of bearing is inversely proportional to the length of the wheel flat and directly proportional to its depth.The paper will contribute to a deeper understanding of the dynamic performance of axle box bearings.