Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum

The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.

All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

All-atom molecular dynamics （MD） simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution. Intramolecular distances, root-mean-square deviation, radius of gyration, and solvent-accessible surface are used to characterize the properties of the carnosine. Carnosine can shift between extended and folded states, but exists mostly in extended state in water. Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance （NMR） experiment. The NMR experimental results are consistent with the molecular dynamics simulations.

Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations

An all-atom dimethyl sulfoxide （DMSO） and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H- ~ ~ O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of （DMSO）m＇S=O…… HW-OW-（H20）n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.

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.

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.

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.

Microstructure of NH4Cl-NH3-H2O System Studied by ATR-FTIR,Raman and MD Simulation

The solubility of ammonium chloride in aqueous ammonia decreases then increases with increasing ammonia concentrations.The molecular mechanism behind this trend is unclear.In this study,ATR-FTIR and Raman spectroscopic techniques were used to determine the effect of ammonium chloride on hydrogen bonding in aqueous ammonia and ultimately explain the observed solubility trend.Spectral analyses were conducted in the wavelength range of 2500-4000 cm^-1 .The results showed that the addition of ammonium chloride endorses the formation of N-H…N hydrogen bonds between ammonium ions and ammonia molecules when the concentration of ammonia is greater than 10% ammonia.However,for concentrations lower than 10%,ammonium ions mainly bond to water molecules,leading to hydrogen bonds of the N-H…O type that are generally less stable than N-H…N bonds.The spectral analyses are confirmed by MD simulations.The results presented herein are useful in the development of novel techniques for the separation of ammonium potassium chloride.

All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.

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.

All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

N,N-dimethylacetamide （DMA） has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions （RDFs） and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding.In this study,we performed large-scale conventional all-atom simulations to complement the folding mechanism of human telomeric sequence Htel24 revealed by a multi-basin hybrid atomistic structure-based model.Firstly,the real time-scale of folding rate,which cannot be obtained from the structure-based simulations,was estimated directly by constructing a Markov state model.The results show that Htel24 may fold as fast as on the order of milliseconds when only considering the competition between the hybrid-1 and hybrid-2 G-quadruplex conformations.Secondly,in comparison with the results of structure-based simulations,more metastable states were identified to participate in the formation of hybrid-1 and hybrid-2 conformations.These findings suggest that coupling the hybrid atomistic structure-based model and the conventional all-atom model can provide more insights into the folding dynamics of DNA G-quadruplex.As a result,the multiscale computational framework adopted in this study may be useful to study complex processes of biomolecules involving large conformational changes.

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.

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.

QUICK ASSESSMENT METHODOLOGY FOR RELIABILITY OF SOLDER JOINTS IN BALL GRID ARRAY(BGA)ASSEMBLY——PART Ⅱ:RELIABILITY EXPERIMENT AND NUMERICAL SIMULATION

In the present study,a facility,i.e.,a mechanical deflection system (MDS),was established and applied to assess the long-term reliability of the solder joints in plastic ball grid array (BGA) assembly.It was found that the MDS not only quickly assesses the long-term reliability of solder joints within days,but can also mimic similar failure mechanisms in accelerated thermal cycling (ATC) tests. Based on the MDS and ATC reliability experiments,the acceleration factors (AF) were obtained for different reliability testing conditions.Furthermore,by using the creep constitutive relation and fatigue life model developed in part I,a numerical approach was established for the purpose of virtual life prediction of solder joints. The simulation results were found to be in good agreement with the test results from the MDS.As a result,a new reliability assessment methodology was established as an alternative to ATC for the evaluation of long-term reliability of plastic BGA assembly.

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.

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.

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.

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 of Plasma Disruptions for HL-2M with the DINA Code

Plasma disruption is often an unavoidable aspect of tokamak operations. It may cause severe damage to in-vessel components such as the vacuum vessel conductors, the first wall and the divertor target plates. Two types of disruption, the hot-plasma vertical displacement event and the major disruption with a cold-plasma vertical displacement event, are simulated by the DINA code for HL-2M. The time evolutions of the plasma current, the halo current, the magnetic axis, the minor radius, the elongation as well as the electromagnetic force and eddy currents on the vacuum vessel during the thermal quench and the current quench are investigated. By comparing the electromagnetic forces before and after the disruption, we find that the disruption causes great damage to the vacuum vessel conductors. In addition, the hot-plasma vertical displacement event is more dangerous than the major disruption with the cold-plasma vertical displacement event.