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.

Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation

In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.

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.

Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond

Nitrogen vacancy(NV)color centers in diamond have useful applications in quantum sensing andfluorescent marking.They can be gen-erated experimentally by ion implantation,femtosecond lasers,and chemical vapor deposition.However,there is a lack of studies of the yield of NV color centers at the atomic scale.In the molecular dynamics simulations described in this paper,NV color centers are pre-pared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing.The differences between the yields of NV color centers produced by implantation of carbon(C)and nitrogen(N)ions,respectively,are investigated.It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy.The effects of different pre-doping concentrations(400–1500 ppm)and implantation energies(1.0–3.0 keV)on the NV color center yield are analyzed,and it is shown that a pre-doping concentra-tion of 1000 ppm with 2 keV C-ion implantation can produce a 13%yield of NV color centers after 1600 K annealing for 7.4 ns.Finally,a brief comparison of the NV color center identification methods is presented,and it is found that the error rate of an analysis utiliz-ing the identify diamond structure coordination analysis method is reduced by about 7%compared with conventional identification+methods.

Molecular Dynamics Numerical Simulation of Adsorption Characteristics and Exploitation Limits in Shale Oil Microscopic Pore Spaces

Microscopic pore structure in continental shale oil reservoirs is characterized by small pore throats and complex micro-structures.The adsorption behavior of hydrocarbons on the pore walls exhibits unique physical and chemical properties.Therefore,studying the adsorption morphology of hydrocarbon components in nanometer-sized pores and clarifying the exploitation limits of shale oil at the microscopic level are of great practical significance for the efficient development of continental shale oil.In this study,molecular dynamics simulations were employed to investigate the adsorption characteristics of various single-component shale oils in inorganic quartz fissures,and the influence of pore size and shale oil hydrocarbon composition on the adsorption properties in the pores was analyzed.The results show that different molecules have different adsorption capacities in shale oil pores,with lighter hydrocarbon components(C6H14)exhibiting stronger adsorption abilities.For the same adsorbed molecule,the adsorption amount linearly increases with the increase in pore diameter,but larger pores contribute more to shale oil adsorption.In shale pores,the thickness of the adsorption layer formed by shale oil molecules ranges from 0.4 to 0.5 nm,which is similar to the width of alkane molecules.Shale oil in the adsorbed state that is difficult to be exploited is mainly concentrated in the first adsorption layer.Among them,the volume fraction of adsorbed shale oil in 6 nm shale pores is 40.8%,while the volume fraction of shale oil that is difficult to be exploited is 16.2%.

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.

CYCLIC HARDENING BEHAVIOR OF POLYCRYSTALS WITH PENETRABLE GRAIN BOUNDARIES:TWO-DIMENSIONAL DISCRETE DISLOCATION DYNAMICS SIMULATION

A two-dimensional discrete dislocation dynamics （DDD） technology by Giessen and Needleman （1995）, which has been extended by integrating a dislocation-grain boundary interaction model, is used to computationally analyze the micro-cyclic plastic response of polycrystals containing micron-sized grains, with special attentions to significant influence of dislocationpenetrable grain boundaries （GBs） on the micro-plastic cyclic responses of polycrystals and underlying dislocation mechanism. Toward this end, a typical polycrystalline rectangular specimen under simple tension-compression loading is considered. Results show that, with the increase of cycle accumulative strain, continual dislocation accumulation and enhanced dislocation-dislocation interactions induce the cyclic hardening behavior; however, when a dynamic balance among dislocation nucleation, penetration through GB and dislocation annihilation is approximately established, cyclic stress gradually tends to saturate. In addition, other factors, including the grain size, cyclic strain amplitude and its history, also have considerable influences on the cyclic hardening and saturation.

Molecular dynamics simulations on the dynamics of two-dimensional rounded squares

The collective motion of rounded squares with different comer-roundness ζ is studied by molecular dynamlcs （MD） simulation in this work. Three types of translational collective motion pattern are observed, including＇, gliding, hopping and a mixture of gliding and hopping. Quantitatively, the dynamics of each observed ordered phase is characterized by both mean square displacement and van Hove functions for both translation and rotation. The effect of corner-roundness on the dynamics is further studied by comparing the dynamics of the rhombic crystal phases folmed by different comer-.rounded particles at a same surface fraction. The results show that as ζ increases from 0.286 to 0.667, the translational collective motion of particles changes from a gliding-dominant pattern to a hopping-dominant patte;n, whereas the rotational motion pattern is hopping-like and does not change in its type, but the rotational hopping becomes much more frequent as increases （i.e., as particles become more rounded）. A simple geometrical model is proposed to explain the trend of gliding motion observed in MD simulations.

Dynamic Simulation of Shear-induced Particle Migration in a Two-dimensional Circular Couette Device

The shear-induced migration of neutrally-buoyant non-colloidal circular particles in a two-dimensional circular Couette flow is investigated numerically with a distributed Lagrange multiplier based fictitious domain method.The effects of inertia and volume fraction on the particle migration are examined.The results indicate that inertia has a negative effect on the particle migration.In consistence with the experimental observations,the rapid migration of particles near the inner cylinder at the early stage is observed in the simulation,which is believed to be related to the chain-like clustering of particles.The migration of circular particles in a plane Poiseuille flow is also examined in order to further confirm the effect of such clustering on the particle migration at early stage.There is tendency for the particles in the vicinity of outer cylinder in the Couette device to pack into concentric rings at late stage in case of high particle concentration.

TWO-DIMENSIONAL NONLINEAR DYNAMIC SYSTEM MODEL OF INTERSPECIFIC INTERACTION AND NUMERICAL SIMULATION RESEARCH ON IT

The mechanism and the course of two_dimensional nonlinear dynamic system of interspecific interaction were dealt with systematically. By extending the Lotka_Volterra model from the viewpoint of biomechanics, it developed new models of two_dimensional nonlinear autonomous and nonautonomous dynamic systems, with its equilibrium point's stability and the existence and stability of its periodical solutions analyzed, and did numerical simulation experiments on its dynamics course. The results show that efficiency of interaction between two populations, time_varying effort, and change direction of action coefficient and reaction coefficient have important influences on the stability of dynamic system, that too large or too small interspecific interaction efficiency and contrary change direction of action coefficient and reaction coefficient may result in the nonstability of the system, and thus it is difficult for two populations to coexist, and that time_varying active force contributes to system stability.

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.