Effects of Fatty Acids on Low-Sulfur Diesel Lubricity:Experimental Investigation, DFT Calculation and MD Simulation

The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re- sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy- droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig （HFRR） meth- od. The efficiency order was supported by the density functional theory （DFT） calculations and the molecular dynamics （MD） simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed films furmed on iron surface. The greater the cohesive energy, the more efficiently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.

MD Simulation of Structural and Mechanical Transformation of Single-Walled Carbon Nanotubes Under Pressure

We investigate the structural and mechanical properties of single-walled carbon nanotubes(SWNTs)under hydrostatic pressure,using constant-pressure molecular dynamics(MD)simulations.We observed that all the SWNTs,independent of their size and chirality,behave like a classical elastic ring exhibiting a buckling transition transforming their cross-sectional shape from a circle to an ellipse.The simulated critical transition pressure agrees well with the prediction from continuum mechanics theory,even for the smallest SWNT with a radius of 0.4nm.Accompanying the buckling shape transition,there is a mechanical hardness transition,upon which the radial moduli of the SWNTs decrease by two orders of magnitude.Further increase of pressure will eventually lead to a second transition from an elliptical to a peanut shape.The ratio of the second shape transition pressure over the first one is found to be very close to a constant of∼1.2,independent of the tube size and chirality.

Interaction specific binding hotspots in Endonuclease colicin-immunity protein complex from MD simulations

The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.

Effects of Fe solid solute on grain boundaries of bi-crystal Cu: A molecular dynamics simulation

Grain boundaries(GBs)play a crucial role on the structural stability and mechanical properties of Cu and its alloys.In this work,molecular dynamics(MD)simulations are employed to study the effects of Fe solutes on the formation energy,excess volume,dislocations and melting behaviors of GBs in CuFe alloys.It is illustrated that Fe solute affects the structural stability of Cu GBs substantially,the formation energy of GBs is reduced,but the thickness and melting point of GBs are increased,that is,the structural stability of Cu GBs is significantly improved owing to the Fe solutes.A strong scaling law exists between the formation energy,excess volume,thickness and melting point of GBs.Therefore,Fe solid solute plays an important role in the characteristics of GBs in bi-crystal Cu.

Metastable hybridized structure transformation in amorphous carbon films during friction-A study combining experiments and MD simulation

Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties.Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction(COF)because of the transformation in bond structure from sp^(3)-C to sp^(2)-C during friction processes.However,the mechanism for such a transformation during friction is not well understood.This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics(MD)simulation.Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear,resulting in a decrease in growth rate of the wear rate after the running-in stage.It is worth noting that the sp^(3)-C atoms were increased during the running-in stage when the films contained lower sp^(3)/sp^(2) ratios.However,the formed sp^(3)-C atoms could only be short-lived and gradually transformed to sp^(2)-C atoms with the graphitization generated on the wearing surface of the films.The radial distribution function and translational order parameter indicated that the films'high sp^(3)/sp^(2) ratio led to an increased sp^(2)-C proportion on the wear scar after friction,which caused an increased structural ordering.

Studies on the Molecular Mechanism between HDAC8 and Inhibitory in Different Bioactivities by Molecular Docking and MD Simulations

HDAC8 is an important target for the treatment of many cancers and other diseases. To develop potent and selective HDAC8 inhibitors, molecular docking and molecular dynamics(MD) simulations were employed for investigation of the mechanism of HDAC8 inhibitions containing hydroxamic acid group. Compound 1 with high activity and compound 2 with low activity were selected for comparative study. Compound 1 formed a stronger chelation with Zn ion and was more stable in the HDAC8 pocket than compound 2. Residues HIS-180, ASP-178, ASP-267, and GLY-140 played a critical role in securing the position of compound 1. Both the head and tail of compound 1 formed strong hydrogen bonds with ASP-178, facilitating the ZBG of compound 1 close to the Zn ion so that they formed permanent chelation during the simulation period. The Cap group of the compounds with branch and long chains was advantageous to form interaction with active pocket opening. What’s more, based on the results of this study, three innovative recommendations for the design of highly active HDAC8 inhibitors were presented, which will be useful for the development of new HDAC8 inhibitors.

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.

Experimental and Molecular Dynamics Simulations for Investigating the Effect of FattyAcid and Its Derivatives on Low Sulfur Diesel Lubricity

In this work,fatty acid and its derivatives were adopted as lubricity additives for low sulfur diesel.Tribological evaluation obtained from the High-Frequency Reciprocating Rig(HFRR)apparatus showed that the lubricating performance of the additives increased in the following order:stearic acid>glycol monopalmitate>stearyl alcohol>ethyl palmitate>cetyl ethyl ether.The adsorption behavior of the additives on Fe(110)surface and Fe2O3(001)surface was investigated by molecular dynamics(MD)simulations to verify their lubricity performance.The results suggested that adsorption energies of the additives on Fe(110)surface are determined by the van der Waals forces,while adsorptions on Fe2O3(001)surface are significantly attributed to the electrostatic attractive forces.Higher values of adsorption energy of the additives on Fe2O3(001)surface indicate that the additive has more efficient lubricity enhancing properties.

Study of sodium lignosulfonate prepare low-rank coal-water slurry:Experiments and simulations

The effect of sodium lignosulfonate(SL)as additive on the preparation of low-rank coal-water slurry(LCWS)was studied by experiments and molecular dynamics(MD)simulation s.The experimental results show that the appropriate amount of additives is beneficial to reduce the viscosity of LCWS and increase the slurry concentration.Adsorption isotherm studies showed that SL conforms to single-layer adsorption on the coal surface,andΔG_(ads)^(0) was negative,proving that the reaction was spontaneous.Zeta potential measurements showed that SL increased the negative charge on coal.FTIR scanning and XPS wide-range scanning were performed on the coal before and after adsorption,and it was found that the content of oxygen functional groups on coal increased after adsorption.Simulation results show that when a large number of SL molecules exist in the solution,some SL molecules will bind to hydrophobic hydrocarbon groups on coal.The rest of the SL molecule s,their hydrophobic alkyl tails,come into contact with each other and aggregate in solution.The agglomeration of SL molecules and the surface of coal with static electricity will also produce electrostatic interaction,which is conducive to the even dispersion of coal particles.The results of mean square displacement(MSD)and self-diffusion coefficient(D)show that the addition of SL reduces the diffusion rate of water molecules.Simulation results correspond to experimental results,indicating that MD simulation is accurate and feasible.

Atomistic simulations of the surface severe plastic deformation-induced grain refinement in polycrystalline magnesium:The effect of processing parameters

Magnesium(Mg)based alloys are promising candidates for many applications,but their untreated surfaces usually have low strength and hardness.In this study,a single point diamond turning(SPDT)technique was applied to refine the grain size and improve the mechanical properties of the surface layers of Mg-Li alloys.By refining grains in the topmost layer to the nanometer scale(~60 nm),the surface hardness was found to be enhanced by approximately 60%.The atomic plastic deformation process during the SPDT was then studied by the real-time atomistic molecular dynamics(MD)simulations.A series of MD simulations with different combinations of parameters,including rake angle,cutting speed and cutting depth,were conducted to understand their influences on the microstructural evolution and associated plastic deformation mechanisms on the surface layer of the workpieces.The MD simulation results suggest that using increased rake angle,cutting speed and cutting depth can help to achieve better grain refinement.These simulation results,which provide atomic-level details of the deformation mechanism,can assist the parameter design for the SPDT techniques to achieve the high-performance heterogeneous nanostructured materials.

Mechanism analysis and simulation of methyl methacrylate production coupled chemical looping gasification system

Nowadays,the efficient and cleaner utilization of coal have attracted wide attention due to the rich coal and rare oil/gas resources structure in China.Coal chemical looping gasification(CCLG)is a promising coal utilization technology to achieve energy conservation and emission reduction targets for highly pure synthesis gas.As a downstream product of synthesis gas,methyl methacrylate(MMA),is widely used as raw material for synthesizing polymethyl methacrylate and resin products with excellent properties.So this paper proposes a novel system integrating MMA production and CCLG(CCLG-MMA)processes aiming at"energy saving and low emission",in which the synthesis gas produced by CCLG and purified by dry methane reforming(DMR)reaction and Rectisol process reacts with ethylene for synthesizing MMA.Firstly,the reaction mechanism of CCLG is investigated by using Reactive force field(ReaxFF)MD simulation based on atomic models of char and oxygen carrier(Fe_(2)O_(3))for obtaining optimum reaction temperature of fuel reactor(FR).Secondly,the steady-state simulation of CCLG-MMA system is carried out to verify the feasibility of MMA production.The amount of CO_(2)emitted by CCLG process and DMR reaction is 0.0028(kg CO_(2))^(-1)·(kg MMA)^(-1).The total energy consumption of the CCLG-MMA system is 45521 kJ·(kg MMA)^(-1),among which the consumption of MMA production part is 25293 k(·kg MMA)^(-1).The results show that the CCLG-MMA system meets CO_(2)emission standard and has lower energy consumption compared to conventional MMA production process.Finally,one control scheme is designed to verify the stability of CCLG-MMA system.The CCLG-MMA integration strategy aims to obtain highly pure MMA from multi-scale simulation perspectives,so this is an optimal design regarding all factors influencing cleaner MMA production.

Simulation on Grain Boundary Sliding during Superplastic Deformation Using Molecular Dynamics Method

Grain growth and grain boundary sliding are the two main superplastic deformation mechanisms. In the paper, simulation work is focused on the sliding of a S3 (111) symmetric twist coincidence grain boundary, a S13 (110) asymmetric tilt coincidence grain boundary, and a S3 (110) symmetric tilt coincidence grain boundary in Al, and the energies of grain boundary for each of equilibrium configurations are computed. An embedded atom method (EAM) potential was used to simulate the atomic interactions in a bicrystal containing more than 2000 atoms. At 0 K, the relationships between total potential energy and time steps for S3 (111) symmetric twist coincidence grain boundary and S3 (110) symmetric tilt coincidence grain boundary during sliding at 2 m/s represent the periodic characteristic. However, the relationship between total potential energy and time steps for S13 (110) asymmetric tilt coincidence grain boundary represents the damp surge characteristic. It is found that grain boundary sliding for S3 (110) symmetric tilt coincidence grain boundary is coupled with apparent grain boundary migration.

Solid−solid phase transition of tungsten induced by high pressure:A molecular dynamics simulation

The phase transition of tungsten(W)under high pressures was investigated with molecular dynamics simulation.The structure was characterized in terms of the pair distribution function and the largest standard cluster analysis(LSCA).It is found that under 40−100 GPa at a cooling rate of 0.1 K/ps a pure W melt first crystallizes into the body-centred cubic(BCC)crystal,and then transfers into the hexagonal close-packed(HCP)crystal through a series of BCC−HCP coexisting states.The dynamic factors may induce intermediate stages during the liquid−solid transition and the criss-cross grain boundaries cause lots of indistinguishable intermediate states,making the first-order BCC−HCP transition appear to be continuous.Furthermore,LSCA is shown to be a parameter-free method that can effectively analyze both ordered and disordered structures.Therefore,LSCA can detect more details about the evolution of the structure in such structure transition processes with rich intermediate structures.

Microstructural evolution and mechanical properties of FeCoCrNiCu high entropy alloys:a microstructure-based constitutive model and a molecular dynamics simulation study

High entropy alloys(HEAs)attract remarkable attention due to the excellent mechanical performance.However,the origins of their high strength and toughness compared with those of the traditional alloys are still hardly revealed.Here,using a microstructure-based constitutive model and molecular dynamics(MD)simulation,we investigate the unique mechanical behavior and microstructure evolution of FeCoCrNiCu HEAs during the indentation.Due to the interaction between the dislocation and solution,the high dislocation density in FeCoCrNiCu leads to strong work hardening.Plentiful slip systems are stimulated,leading to the good plasticity of FeCoCrNiCu.The plastic deformation of FeCoCrNiCu is basically affected by the motion of dislocation loops.The prismatic dislocation loops inside FeCoCrNiCu are formed by the dislocations with the Burgers vectors of a/6[112]and a/6[112],which interact with each other,and then emit along the<111>slip direction.In addition,the mechanical properties of FeCoCrNiCu HEA can be predicted by constructing the microstructure-based constitutive model,which is identified according to the evolution of the dislocation density and the stress-strain curve.Strong dislocation strengthening and remarkable lattice distortion strengthening occur in the deformation process of FeCoCrNiCu,and improve the strength.Therefore,the origins of high strength and high toughness in FeCoCrNiCu HEAs come from lattice distortion strengthening and the more activable slip systems compared with Cu.These results accelerate the discovery of HEAs with excellent mechanical properties,and provide a valuable reference for the industrial application of HEAs.

Theoretical studies and molecular dynamics simulations on ion transport properties in nanochannels and nanopores

Control of ion transport and fluid flow through nanofluidic devices is of primary importance for energy storage and conversion, drug delivery and a wide range of biological processes. Recent development of nanotechnology, synthesis techniques, purification technologies, and experiment have led to rapid advances in simulation and modeling studies on ion transport properties. In this review, the applications of Poisson-Nernst-Plank （PNP） equations in analyzing transport properties are presented. The molecular dynamics （MD） studies of transport properties of ion and fluidic flow through nanofluidic devices are reported as well.

Studies on the Structures and Hydrogen-bonding Interactions in Aqueous Glycine Solutions Using All-atom Molecular Dynamics Simulations and NMR Spectroscopy

All-atom molecular dynamics （MD） simulations and chemical shifts were used to study interactions and structures in the glycine-water system. Radial distribution functions and the hydrogen-bond network were applied in MD simulations. Aggregates in the aqueous glycine solution could be classified into different regions by analysis of the hydrogen-bonding network. Temperature-dependent NMR spectra and the viscosity of glycine in aqueous solutions were measured to compare with the results of MD simulations. The variation tendencies of the hydrogen atom chemical shifts and viscosity with concentration of glycine agree with the statistical results of hydrogen bonds in the MD simulations.

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.

Reactive molecular dynamics insight into the thermal decomposition mechanism of 2,6-Bis(picrylamino)-3,5-dinitropyridine

2,6-bis(picrylamino)-3,5-dinitropyridine(PYX)has excellent thermostability,which makes its thermal decomposition mechanism receive much attention.In this paper,the mechanism of PYX thermal decomposition was investigated thoroughly by the ReaxFF-lg force field combined with DFT-B3LYP(6-311++G)method.The detailed decomposition mechanism,small-molecule product evolution,and cluster evolution of PYX were mainly analyzed.In the initial stage of decomposition,the intramolecular hydrogen transfer reaction and the formation of dimerized clusters are earlier than the denitration reaction.With the progress of the reaction,one side of the bitter amino group is removed from the pyridine ring,and then the pyridine ring is cleaved.The final products produced in the thermal decomposition process are CO_(2),H_(2)O,N_(2),and H_(2).Among them,H_(2)O has the earliest generation time,and the reaction rate constant(k_(3))is the largest.Many clusters are formed during the decomposition of PYX,and the formation,aggregation,and decomposition of these clusters are strongly affected by temperature.At low temperatures(2500 K-2750 K),many clusters are formed.At high temperatures(2750 K-3250 K),the clusters aggregate to form larger clusters.At 3500 K,the large clusters decompose and become small.In the late stage of the reaction,H and N in the clusters escaped almost entirely,but more O was trapped in the clusters,which affected the auto-oxidation process of PYX.PYX's initial decomposition activation energy(E_(a))was calculated to be 126.58 kJ/mol.This work contributes to a theoretical understanding of PYX's entire thermal decomposition process.

Recent Progress in Superhydrophobic Coatings Using Molecular Dynamics Simulations and Experimental Techniques

Superhydrophobic(SH)coatings are intended to resist a surface from cor­rosion and thereby increases the product life duration.It is also a promising solution to save cleaning costs and time by providing self-clean nature to the surface.This review article provides the most recent updates in design­ing SH surfaces and their characterizations adopted both in experimental and computational techniques.To gain a comprehensive perspective,the SH surfaces present in nature those are inspiring human beings to mimic such surfaces are introduced at the beginning of this article.Subsequently,different fabrication techniques undertaken recently to design artificial SH surfaces are briefly discussed.Recent progress in computations employed in the development of SH surfaces is then discussed.Next,the limitations in SH surfaces are addressed.Finally,perceptiveness of different strategies and their limitations are presented in the concluding remarks and outlook.Overall,this mini review article brings together and highlights the significant advancements in fabrication of superhydrophobic surfaces which may surely help the early-stage researchers/scientists to plan their work accordingly.

Lamellar water induced quantized interlayer spacing of nanochannels walls

The nanoscale confinement is of great important for the industrial applications of molecular sieve,desalination,and also essential in bio-logical transport systems.Massive efforts have been devoted to the influence of restricted spaces on the properties of confined fluids.However,the situation of channel-wall is crucial but attracts less attention and remains unknown.To fundamentally understand the mechanism of channel-walls in nanoconfinement,we investigated the interaction between the counter-force of the liquid and interlamellar spacing of nanochannel walls by considering the effect of both spatial confinement and surface wettability.The results reveal that the nanochannel stables at only a few discrete spacing states when its confinement is within 1.4 nm.The quantized interlayer spacing is attributed to water molecules becoming laminated structures,and the stable states are corresponding to the monolayer,bilayer and trilayer water configurations,respectively.The results can potentially help to understand the characterized interlayers spacing of graphene oxide membrane in water.Our findings are hold great promise in design of ion filtration membrane and artificial water/ion channels.