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molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

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Chinese Physics B 2024年第2期33卷 512-521页

作者：徐耀黄舒伟丁泓铭马余强 National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Center for Soft Condensed Matter Physics and Interdisciplinary Research School of Physical Science and TechnologySoochow UniversitySuzhou 215006China

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

关键词： RNA DNA lipid bilayer molecular dynamics interface interaction divalent cation

Micro-mechanism Study on the Different Antioxidants Protective Effect of Vegetable Oil by ReaxFF molecular dynamics

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CSEE Journal of Power and Energy Systems 2024年第3期10卷 1269-1279页

作者： Haoxi Cong Xuefeng Hu Hao Pan Qingmin Li State Key Laboratory of Alternate Electrical Power System With Renewable Energy Sources North China Electric Power UniversityBeijing 102206China

The aging problem of vegetable oil has severely restricted the popularization and application of vegetable oil transformers.Adding antioxidants is the most recommended solution.At present,there is insufficient research on the micromechanism application of the protective effect of antioxidants on vegetable oil.In this paper,multiple vegetable oil models with different types and concentrations of antioxidants are established.Then the molecular dynamics simulation based on ReaxFF is carried out at different temperatures and oxygen content.Results show that the protective mechanism of antioxidants is to release H and combine this with free radicals generated by the decomposition of unsaturated fatty acids(UFA)in the oil.In addition,the protective effects of four antioxidants show different results.The stronger ones are tert-butyl hydroquinone(TBHQ)and butylated hydroxytoluene(BHT),while the weaker ones are butylated hydroxyanisole(BHA)and propyl gallate(PG).TBHQ has a better protective effect at lower concentrations,but the decomposition of UFA is promoted at higher concentrations.When the temperature rises,the decomposition of UFA is promoted.With the addition of oxygen,smaller molecular compounds are easily oxidized,and the decomposition of UFA is accelerated.The above research could reveal the microscopic mechanism of antioxidant protection on vegetable oil,providing theoretical references for further exploration of effective vegetable oil aging protection technology.

关键词： Antioxidant molecular dynamics transformer vegetable oil

Probing the electric double layer structure at nitrogen-doped graphite electrodes by constant-potential molecular dynamics simulations

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Journal of Energy Chemistry 2024年第6期93卷 299-305,I0008页

作者： Legeng Yu Nan Yao Yu-Chen Gao Zhong-Heng Fu Bo Jiang Ruiping Li Cheng Tang Xiang Chen Tsinghua Center for Green Chemical Engineering Electrification(CCEE) Department of Chemical EngineeringTsinghua UniversityBeijing 100084China Beijing Advanced Innovation Center for Materials Genome Engineering Institute for Advanced Materials and TechnologyUniversity of Science and Technology BeijingBeijing 100083China National Materials Corrosion and Protection Data Center University of Science and Technology BeijingBeijing 100083China Ordos Carbon Neutral Research and Application Co. Ltd.Ordos 017010Inner Mongoli1China Institute for Carbon Neutrality Tsinghua UniversityBeijing 100084China Center for Next-Generation Energy Materials and School of Chemical Engineering Sungkyunkwan University2066 Seobu-roJangan-guSuwon-siGyeonggi-do 16419Republic of Korea

Electric double layer(EDL)is a critical topic in electrochemistry and largely determines the working performance of lithium batteries.However,atomic insights into the EDL structures on heteroatom-modified graphite anodes and EDL evolution with electrode potential are very lacking.Herein,a constant-potential molecular dynamics(CPMD)method is proposed to probe the EDL structure under working conditions,taking N-doped graphite electrodes and carbonate electrolytes as an example.An interface model was developed,incorporating the electrode potential and atom electronegativities.As a result,an insightful atomic scenario for the EDL structure under varied electrode potentials has been established,which unveils the important role of doping sites in regulating both the EDL structures and the following electrochemical reactions at the atomic level.Specifically,the negatively charged N atoms repel the anions and adsorb Li~+at high and low potentials,respectively.Such preferential adsorption suggests that Ndoped graphite can promote Li~+desolvation and regulate the location of Li~+deposition.This CPMD method not only unveils the mysterious function of N-doping from the viewpoint of EDL at the atomic level but also applies to probe the interfacial structure on other complicated electrodes.

关键词： Lithium batteries Graphite N-doping Electric double layer molecular dynamics Constant potential method Electrode potential

Exploring the Effect of Plasticity on the Phase Imaging of TM-AFM Through molecular dynamics Simulations

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Acta Mechanica Solida Sinica 2024年第2期37卷 297-304页

作者： Guolin Liu Yu Zeng Yaxin Chen Zheng Wei School of Mechanical and Electrical Engineering Beijing University of Chemical TechnologyBeijing100029China

In the tapping-mode atomic force microscope(TM-AFM),the probe tip continuously taps the sample surface,which may cause plastic deformation of the sample and result in energy dissipation.The energy dissipation of the probe is closely related to the scanned phase image.To quantify the energy dissipation due to plastic indentations of the sample,this study utilized a combination of molecular dynamics(MD)simulations and experiments on single-crystal copper samples,including multiple nano-indentation tests.The energy dissipation of the probe due to the plastic deformation of the sample was calculated by integrating the hysteresis curve of the indentation depth versus the force applied to the indenter.The simulation results are in good agreement with the experimental ones.Both sets of results have demonstrated that the plastic energy dissipation decreases as the number of indentations increases,and eventually the energy of the probe tends to stabilize.This equilibrium energy dissipation is associated with other dissipation mechanisms.Furthermore,it was observed that,after hundreds of taps,the dissipated energy of plastic deformation could be ignored,implying that the scanned image may not reflect the plasticity information of the sample after multiple taps of the probe on the sample surface for scanning.

关键词： Atomic force microscopy Force-distance curves Nano-indentations Plasticity molecular dynamics

Revealing Al-O/Al-F reaction dynamic effects on the combustion of aluminum nanoparticles in oxygen/fluorine containing environments:A reactive molecular dynamics study meshing together experimental validation

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Defence Technology（防务技术） 2024年第4期34卷 313-327页

作者： Gang Li Chuande Zhao Qian Yu Fang Yang Jie Chen Institute of Chemical Materials China Academy of Engineering Physics(CAEP)P.O.Box 919-311Mianyang 621900SichuanChina

Improving the energy conversion efficiency in metallic fuel(e.g.,Al)combustion is always desirable but challenging,which often involves redox reactions of aluminum(Al)with various mixed oxidizing environments.For instance,Al-O reaction is the most common pathway to release limited energy while Al-F reaction has received much attentions to enhance Al combustion efficiency.However,microscopic understanding of the Al-O/Al-F reaction dynamics remains unsolved,which is fundamentally necessary to further improve Al combustion efficiency.In this work,for the first time,Al-O/Al-F reaction dynamic effects on the combustion of aluminum nanoparticles(n-Al)in oxygen/fluorine containing environments have been revealed via reactive molecular dynamics(RMD)simulations meshing together combustion experiments.Three RMD simulation systems of Al core/O_(2)/HF,n-Al/O_(2)/HF,and n-Al/O_(2)/CF4 with oxygen percentage ranging from 0%to 100%have been performed.The n-Al combustion in mixed O_(2)/CF_4 environments have been conducted by constant volume combustion experiments.RMD results show that Al-O reaction exhibits kinetic benefits while Al-F reaction owns thermodynamic benefits for n-Al combustion.In n-Al/O_(2)/HF,Al-O reaction gives faster energy release rate than Al-F reaction(1.1 times).The optimal energy release efficiency can be achieved with suitable oxygen percentage of 10%and 50%for n-Al/O_(2)/HF and n-Al/O_(2)/CF_4,respectively.In combustion experiments,90%of oxygen percentage can optimally enhance the peak pressure,pressurization rate and combustion heat.Importantly,Al-O reaction prefers to occur on the surface regions while Al-F reaction prefers to proceed in the interior regions of n-Al,confirming the kinetic/thermodynamic benefits of Al-O/Al-F reactions.The synergistic effect of Al-O/Al-F reaction for greatly enhancing n-Al combustion efficiency is demonstrated at atomicscale,which is beneficial for optimizing the combustion performance of metallic fuel.

关键词： Al-O/Al—F reaction Kinetic benefits Thermodynamic benefits molecular dynamics Combustion

molecular dynamics, Diffusion Coefficients and Activation Energy of the Electrolyte (Anode) in Lithium (Li and Li⁺), Sodium (Na and Na⁺) and Potassium (K and K⁺)

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Modeling and Numerical Simulation of Material Science 2024年第1期14卷 39-57页

作者： Alain Second Dzabana Honguelet Timothée Nsongo Bitho Rodongo Earvin Loumbandzila Faculty of Science and Technology Marien Ngouabi University Brazzaville Congo Research Group on The Physical and Chemical Properties of Materials Brazzaville Congo Association Alpha Sciences Beta Technologies Brazzaville Congo Centre for Geological and Mining Research Brazzaville Congo

This work is a simulation modelling with the LAMMPS calculation code of an electrode based on alkali metals (lithium, sodium and potassium) using the MEAM potential. For different multiplicities, two models were studied;with and without gap. In this work, we present the structural, physical and chemical properties of the lithium, sodium and potassium electrodes. For the structural properties, the cohesive energy and the mesh parameters were calculated, revealing that, whatever the chemical element selected, the compact hexagonal hcp structure is the most stable, followed by the face-centred cubic CFC structure, and finally the BCC structure. The most stable structure is lithium, with a cohesion energy of -6570 eV, and the lowest bcc-hcp transition energy of -0.553 eV/atom, followed by sodium. For physical properties, kinetic and potential energies were calculated for each of the sectioned chemical elements, with lithium achieving the highest value. Finally, for the chemical properties, we studied the diffusion coefficient and the activation energy. Only potassium followed an opposite order to the other two, with the quantities with lacunae being greater than those without lacunae, whatever the multiplicity. The order of magnitude of the diffusion coefficients is given by the relationship DLi > DNa > Dk for the multiplicity 6*6*6, while for the activation energy the order is reversed.

关键词： molecular dynamics Diffusion Coefficients Activation Energy Lithium Alkali Metals MEAM Potential

Semiclassical approach to spin dynamics of a ferromagnetic S = 1 chain

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Chinese Physics B 2024年第6期33卷 95-100页

作者：李承晨崔祎于伟强俞榕 Department of Physics and Beijing Key Laboratory of Opto-electronic Functional Materials and Micro-nano Devices Renmin University of ChinaBeijing 100872China Key Laboratory of Quantum State Construction and Manipulation(Ministry of Education) Renmin University of ChinaBeijing 100872China

Motivated by recent experimental progress on the quasi-one-dimensional quantum magnet Ni Nb2O6, we study the spin dynamics of an S = 1 ferromagnetic Heisenberg chain with single-ion anisotropy by using a semiclassical molecular dynamics approach. This system undergoes a quantum phase transition from a ferromagnetic to a paramagnetic state under a transverse magnetic field, and the magnetic response reflecting this transition is well described by our semiclassical method.We show that at low temperature the transverse component of the dynamical structure factor depicts clearly the magnon dispersion, and the longitudinal component exhibits two continua associated with single-and two-magnon excitations,respectively. These spin excitation spectra show interesting temperature dependence as effects of magnon interactions. Our findings shed light on the experimental detection of spin excitations in a large class of quasi-one-dimensional magnets.

关键词： one-dimensional ferromagnetism spin dynamics magnon excitation molecular dynamics

molecular dynamics study on mechanical behaviors of Ti/Ni nanolaminate with a pre-existing void

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Nano Materials Science 2022年第2期4卷 113-125页

作者： Mengjia Su Qiong Deng Lanting Liu Lianyang Chen He He Yinggang Miao Joint International Research Laboratory of Impact dynamics and Its Engineering Applications School of AeronauticsNorthwestern Polytechnical UniversityXi'anShaanxi 710072China

Metallic nanolaminated materials possess excellent mechanical properties due to their unique modulation structures and interfacial properties.However,how microdefects affect their mechanical properties is still uncertain.To evaluate the influences of void location(in the crystalline layer and the Ti/Ni interface),void diameter(d)and thickness of the intermediate layer(h)on overall tensile behaviors,various types of defective Ti/Ni nanolaminates with pre-existing void are established by the molecular dynamics method in this work.The results indicate that the strength and plastic deformation mechanisms are strongly dependent on those determinants.Yield stresses of Ti/Ni nanolaminates decrease distinctly with increasing void diameter,while peak stresses with a void in the crystalline layer decrease with increasing d/h.Different void locations lead eventually to disparate initial plastic deformation carriers around the void,and various evolutions in the microstructure of the defective Ti/Ni nanolaminates.The Ti/Ni interface plays a significant role in the tensile process.The semi-coherent interface impedes new grains and lattice dislocations from passing across the interface,while the incoherent interface facilitates dislocations generating and sliding along the interface,and absorbs the dislocations moving to the interface.The results also indicate that the strain rate significantly affects the evolution of the microstructure and the tensile properties of defective Ti/Ni nanolaminates.

关键词： Defective Ti/Ni nanolaminate Pre-existing void Interface Tensile behaviors molecular dynamics

molecular dynamics simulation and micropillar compression of deformation behavior in iridium single crystals

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Rare Metals 2023年第10期42卷 3510-3517页

作者： Jia-Qi Wu Rui Hu Jie-Ren Yang Bin Gan Gong-Liao Luo Yi Liu Xi-Ming Luo State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi’an710072China State Key Laboratory of Advanced Technologies for Comprehensive Utilization of Platinum Metal Sino-platinum Metals Co.Ltd.Kunming Institute of Precious MetalsKunming650106China

The compression behaviors of iridium single crystals with different crystalline orientations were investigated by micropillar compression tests and molecular dynamics(MD) simulations.The results indicated that the deformation process of iridium single crystals with [100]and [110] orientations was presented as the stacking faults expansion and the formation of Lomer-Cottrell locks.And the occurrence of Lomer-Cottrell locks was considered as the interaction of stacking faults on {111} planes by MD simulations.The evolution of crystal structure in compression indicated that the Lomer-Cottrell locks might contribute to the large plastic deformation of iridium single crystals.Moreover,the deformation features in MD simulations showed that the elastic modulus(E) and yield stress(σ_(s)) of iridium single crystals were significantly influenced by the temperature.The elastic modulus and yield stress gradually decreased with an increased temperature for all orientations.Meanwhile,the single crystal with a closely spaced lattice structure exhibited superior mechanical properties at a same temperature.

关键词： Iridium single crystal Crystalline orientation Deformation behavior molecular dynamics Micropillar compression