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Predicting bioactive compounds and cancer-related molecular targets of lotus seedpod (Receptaculum Nelumbinis) based on network pharmacology and molecular docking
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作者 Jian-Lin Shen Meng-Tong Zhang +8 位作者 Fei Li Jia-Yu Huang Quan-Sheng Xu Han-Yue Zhang Jun Zhang Jing Li Yan-Ping Li Qi Zou Xiao-Yin Wang 《Food and Health》 2024年第2期14-41,共28页
Background:Lotus seedpod(Receptaculum Nelumbinis)is the abundant by-products produced during lotus seed processing,and the sources are usually considered to be wastes and are abandoned outdoors or incinerated.This stu... Background:Lotus seedpod(Receptaculum Nelumbinis)is the abundant by-products produced during lotus seed processing,and the sources are usually considered to be wastes and are abandoned outdoors or incinerated.This study aims at predicting its bioactive compounds and cancer-related molecular targets against six cancers,including lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.Methods:Network pharmacology and molecular docking methods were performed.Results:Network pharmacology results indicated that 14 core compounds(liensinine,tetrandrine,lysicamine,tricin,sanleng acid,cireneol G,ricinoleic acid,linolenic acid,5,7-dihydroxycoumarin,apigenin,luteolin,morin,quercetin and isorhamnetin)and 10 core targets(AKT1,ESR1,HSP90AA1,JUN,MAPK1,MAPK3,PIK3CA,PIK3R1,SRC and STAT3)were screened for lotus seedpod against the six cancers.Molecular docking analysis suggested that the binding abilities between the core compounds and the core targets were mostly strong.GO analysis revealed that the intersected targets between the bioactive compounds of lotus seedpod and the six cancers were significantly related to biological processes,cell compositions and molecular functions.KEGG analysis showed that PI3K-Akt,TNF,Ras,MAPK,HIF-1 and C-type lectin receptor signaling pathways were notably involved in the anti-cancer activities of lotus seedpod against the six cancers.Conclusions:14 core compounds and 10 core targets were screened for lotus seedpod against lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.This study supports the application of lotus seedpod in treating cancers,and promotes the recycling and the high-value utilization. 展开更多
关键词 Lotus seedpod ANTI-CANCER Bioactive compounds molecular targets Network pharmacology molecular docking.
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Novel umami peptides from two Termitomyces mushrooms and molecular docking to the taste receptor T1R1/T1R3 被引量:1
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作者 Lanyun Zhang Li Zhang +3 位作者 Jesus Pérez-Moreno Lu Bin Fengming Zhang Fuqiang Yu 《Food Science and Human Wellness》 SCIE CSCD 2024年第2期1055-1064,共10页
Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces... Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces aff.bulborhizus.Ten umami peptides from aqueous extracts were separated using a Sephadex G-15 gel filtration chromatography.The intense umami fraction was evaluated by both sensory evaluation and electronic tongue.They were identified as KLNDAQAPK,DSTDEKFLR,VGKGAHLSGEH,MLKKKKLA,SLGFGGPPGY,TVATFSSSTKPDD,AMDDDEADLLLLAM,VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK.Seven peptides,except VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK were selectively synthesized to verify their taste characteristics.All these 10 peptides had umami or salt taste.The 10 peptides were conducted by molecular docking to study their interaction with identified peptides and the umami taste receptor T1R1/T1R3.All these 10 peptides perfectly docked the active residues in the T1R3 subunit.Our results provide theoretical basis for the umami taste and address the umami mechanism of two wild edible Termitomyces mushrooms. 展开更多
关键词 TERMITOMYCES Non-volatile flavor compounds Umami peptides Taste characteristics molecular docking
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Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis
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作者 Sze Wan Hung Massimiliano Gaetani +12 位作者 Yiran Li Zhouyurong Tan Xu Zheng Ruizhe Zhang Yang Ding Gene Chi Wai Man Tao Zhang Yi Song Yao Wang Jacqueline Pui Wah Chung Tak Hang Chan Roman A.Zubarev Chi Chiu Wang 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2024年第1期100-114,共15页
Endometriosis is a common chronic gynecological disease with endometrial cell implantation outside the uterus.Angiogenesis is a major pathophysiology in endometriosis.Our previous studies have demonstrated that the pr... Endometriosis is a common chronic gynecological disease with endometrial cell implantation outside the uterus.Angiogenesis is a major pathophysiology in endometriosis.Our previous studies have demonstrated that the prodrug of epigallocatechin gallate(ProEGCG)exhibits superior anti-endometriotic and anti-angiogenic effects compared to epigallocatechin gallate(EGCG).However,their direct binding targets and underlying mechanisms for the differential effects remain unknown.In this study,we demonstrated that oral ProEGCG can be effective in preventing and treating endometriosis.Additionally,1D and 2D Proteome Integral Solubility Alteration assay-based chemical proteomics identified metadherin(MTDH)and PX domain containing serine/threonine kinase-like(PXK)as novel binding targets of EGCG and ProEGCG,respectively.Computational simulation and BioLayer interferometry were used to confirm their binding affinity.Our results showed that MTDH-EGCG inhibited protein kinase B(Akt)-mediated angiogenesis,while PXK-ProEGCG inhibited epidermal growth factor(EGF)-mediated angiogenesis via the EGF/hypoxia-inducible factor(HIF-1a)/vascular endothelial growth factor(VEGF)pathway.In vitro and in vivo knockdown assays and microvascular network imaging further confirmed the involvement of these signaling pathways.Moreover,our study demonstrated that ProEGCG has superior therapeutic effects than EGCG by targeting distinct signal transduction pathways and may act as a novel antiangiogenic therapy for endometriosis. 展开更多
关键词 molecular targets ProEGCG EGCG ANGIOGENESIS TREATMENT ENDOMETRIOSIS
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Absorption characteristics,model,and molecular mechanism of hydrogen sulfide in morpholine acetate aqueous solution
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作者 Hongwei Jin Yun Teng +8 位作者 Kangkang Li Zhou Feng Zhonghao Li Shiqi Qu Hongzhi Xia Huanong Cheng Yugang Li Xinshun Tan Shiqing Zheng 《Chinese Journal of Chemical Engineering》 SCIE EI CAS CSCD 2024年第2期125-135,共11页
The solubility of H_(2)S was measured in solutions of N-butyl-N-methylmorpholine acetate([Bmmorp][Ac])containing 20%-40%(mass)water at experimental temperatures ranged from 298.15 to 328.15 K and pressures up to 320 k... The solubility of H_(2)S was measured in solutions of N-butyl-N-methylmorpholine acetate([Bmmorp][Ac])containing 20%-40%(mass)water at experimental temperatures ranged from 298.15 to 328.15 K and pressures up to 320 k Pa.The total solubility of H_(2)S increased with higher temperatures,lower pressures,and reduced water content.The reaction equilibrium thermodynamic model was used to correlate the solubility data.The results indicate that the chemical reaction equilibrium constant decrease with increasing water content and temperature,whereas Henry constant increase with increasing water content and temperature.Compared with other ionic liquids,H_(2)S exhibits a higher physical absorption enthalpy and a lower chemical absorption enthalpy in[Bmmorp][Ac]aqueous solution.This suggests that[Bmmorp][Ac]has a strong physical affinity for H_(2)S and low energy requirement for desorption.Quantum chemical methods were used to investigate the molecular mechanism of H_(2)S absorption in ionic liquids.The interaction energy analysis revealed that the binding of H_(2)S with the ionic liquid in a1:2 ratio is more stable.Detailed analyses by the methods of the interaction region indicator and the atoms in molecules were conducted to the interactions between H_(2)S and the ionic liquid. 展开更多
关键词 Ionic liquid Hydrogen sulfide MODEL SOLUBILITY molecular mechanism
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Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer
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作者 徐耀 黄舒伟 +1 位作者 丁泓铭 马余强 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第2期512-521,共10页
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,... 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. 展开更多
关键词 RNA DNA lipid bilayer molecular dynamics interface interaction divalent cation
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Molecular dynamics simulation of the flow mechanism of shear-thinning fluids in a microchannel
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作者 杨刚 郑庭 +1 位作者 程启昊 张会臣 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第4期516-525,共10页
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... 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. 展开更多
关键词 molecular dynamics simulation non-Newtonian fluid MICROCHANNEL SHEAR-THINNING
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Effect of Molecular Weight on Thermoelectric Performance of P3HT Analogues with 2-Propoxyethyl Side Chains
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作者 董得福 WANG Wei +3 位作者 ZHAN Chun LI Chenglong ZHOU Qisheng 肖生强 《Journal of Wuhan University of Technology(Materials Science)》 SCIE EI CAS CSCD 2024年第2期268-281,共14页
By replacing hexyl chains in poly(3-hexylthiophene)(P3HT)with 2-propoxyethyls,four poly(3-(2-propoxyethyl)thiophene)(P3POET)homopolymers with comparable polydispersity indexes(PDI)and regioregularities were prepared h... By replacing hexyl chains in poly(3-hexylthiophene)(P3HT)with 2-propoxyethyls,four poly(3-(2-propoxyethyl)thiophene)(P3POET)homopolymers with comparable polydispersity indexes(PDI)and regioregularities were prepared herein in addition with step increment of about 7 kDa on numberaverage molecular weight(M_(n))from around 11 to 32 kDa(accordingly denoted as P11k,P18k,P25k,and P32k).When doped in film by FeCl_(3)at the optimized conditions,the maximum power factor(PF_(max))increases greatly from 4.3μW·m^(-1)·K^(-2)for P11k to 8.8μW·m^(-1)·K^(-2)for P18k,and further to 9.7μW·m^(-1)·K^(-2)for P25k,followed by a slight decrease to 9.2μW·m^(-1)·K^(-2)for P32k.The close Seebeck coefficients(S)at PF_(max)are observed in these doped polymer films due to their consistent frontier orbital energy levels and Fermi levels.The main contribution to this PF_(max)evolution thus comes from the corresponding conductivities(σ).Theσvariation of the doped films can be rationally correlated with their microstructure evolution. 展开更多
关键词 conjugated polymer molecular weight MICROSTRUCTURE thermoelectric performance
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Temperature effect on nanotwinned Ni under nanoindentation using molecular dynamic simulation
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作者 何茜 徐子翼 倪玉山 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第1期603-612,共10页
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... 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. 展开更多
关键词 NANOINDENTATION twin boundary plastic deformation molecular dynamics simulation
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Analysis of CH_(4) and H_(2) Adsorption on Heterogeneous Shale Surfaces Using aMolecular Dynamics Approach
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作者 Surajudeen Sikiru Hassan Soleimani +2 位作者 Amir Rostami Mohammed Falalu Hamza Lukmon Owolabi Afolabi 《Fluid Dynamics & Materials Processing》 EI 2024年第1期31-44,共14页
Determining the adsorption of shale gas on complex surfaces remains a challenge in molecular simulation studies.Difficulties essentially stem from the need to create a realistic shale structure model in terms of miner... Determining the adsorption of shale gas on complex surfaces remains a challenge in molecular simulation studies.Difficulties essentially stem from the need to create a realistic shale structure model in terms of mineral heterogeneityand multiplicity.Moreover,precise characterization of the competitive adsorption of hydrogen andmethane in shale generally requires the experimental determination of the related adsorptive capacity.In thisstudy,the adsorption of adsorbates,methane(CH_(4)),and hydrogen(H_(2))on heterogeneous shale surface modelsof Kaolinite,Orthoclase,Muscovite,Mica,C_(60),and Butane has been simulated in the frame of a moleculardynamic’s numerical technique.The results show that these behaviors are influenced by pressure and potentialenergy.On increasing the pressure from 500 to 2000 psi,the sorption effect for CH_(4)significantly increasesbut shows a decline at a certain stage(if compared to H_(2)).The research findings also indicate that raw shalehas a higher capacity to adsorb CH_(4)compared to hydrogen.However,in shale,this difference is negligible. 展开更多
关键词 Shale gas ADSORPTION METHANE hydrogen molecular dynamic SORPTION
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Optimization of Cooperative RelayingMolecular Communications for Nanomedical Applications
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作者 Eman S.Attia Ashraf A.M.Khalaf +4 位作者 Fathi E.Abd El-Samie Saied M.Abd El-atty Konstantinos A.Lizos Osama Alfarraj Heba M.El-Hoseny 《Computer Modeling in Engineering & Sciences》 SCIE EI 2024年第2期1259-1275,共17页
Recently,nano-systems based on molecular communications via diffusion(MCvD)have been implemented in a variety of nanomedical applications,most notably in targeted drug delivery system(TDDS)scenarios.Furthermore,becaus... Recently,nano-systems based on molecular communications via diffusion(MCvD)have been implemented in a variety of nanomedical applications,most notably in targeted drug delivery system(TDDS)scenarios.Furthermore,because the MCvD is unreliable and there exists molecular noise and inter symbol interference(ISI),cooperative nano-relays can acquire the reliability for drug delivery to targeted diseased cells,especially if the separation distance between the nano transmitter and nano receiver is increased.In this work,we propose an approach for optimizing the performance of the nano system using cooperative molecular communications with a nano relay scheme,while accounting for blood flow effects in terms of drift velocity.The fractions of the molecular drug that should be allocated to the nano transmitter and nano relay positioning are computed using a collaborative optimization problem solved by theModified Central Force Optimization(MCFO)algorithm.Unlike the previous work,the probability of bit error is expressed in a closed-form expression.It is used as an objective function to determine the optimal velocity of the drug molecules and the detection threshold at the nano receiver.The simulation results show that the probability of bit error can be dramatically reduced by optimizing the drift velocity,detection threshold,location of the nano-relay in the proposed nano system,and molecular drug budget. 展开更多
关键词 Nanomedical system molecular communication cooperative relay OPTIMIZATION
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Comparative study on phase transition behaviors of fractional molecular field theory and random-site Ising model
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作者 刘婷玉 赵薇 +3 位作者 王涛 安小冬 卫来 黄以能 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期536-541,共6页
Fractional molecular field theory(FMFT)is a phenomenological theory that describes phase transitions in crystals with randomly distributed components,such as the relaxor-ferroelectrics and spin glasses.In order to ver... Fractional molecular field theory(FMFT)is a phenomenological theory that describes phase transitions in crystals with randomly distributed components,such as the relaxor-ferroelectrics and spin glasses.In order to verify the feasibility of this theory,this paper fits it to the Monte Carlo simulations of specific heat and susceptibility versus temperature of two-dimensional(2D)random-site Ising model(2D-RSIM).The results indicate that the FMFT deviates from the 2D-RSIM significantly.The main reason for the deviation is that the 2D-RSIM is a typical system of component random distribution,where the real order parameter is spatially heterogeneous and has no symmetry of space translation,but the basic assumption of FMFT means that the parameter is spatially uniform and has symmetry of space translation. 展开更多
关键词 phase transition molecular field theory Ising model Monte Carlo
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Integrating Levels of Hierarchical Organization in Porous Organic Molecular Materials
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作者 Jesus Ferrando‑Soria Antonio Fernandez 《Nano-Micro Letters》 SCIE EI CAS CSCD 2024年第5期134-153,共20页
Porous organic molecular materials(POMMs)are an emergent class of molecular-based materials characterized by the formation of extended porous frameworks,mainly held by non-covalent interactions.POMMs represent a varie... Porous organic molecular materials(POMMs)are an emergent class of molecular-based materials characterized by the formation of extended porous frameworks,mainly held by non-covalent interactions.POMMs represent a variety of chemical families,such as hydrogen-bonded organic frameworks,porous organic salts,porous organic cages,C-H···πmicroporous crystals,supramolecular organic frameworks,π-organic frameworks,halogen-bonded organic framework,and intrinsically porous molecular materials.In some porous materials such as zeolites and metal organic frameworks,the integration of multiscale has been adopted to build materials with multifunctionality and optimized properties.Therefore,considering the significant role of hierarchy in porous materials and the growing importance of POMMs in the realm of synthetic porous materials,we consider it appropriate to dedicate for the first time a critical review covering both topics.Herein,we will provide a summary of literature examples showcasing hierarchical POMMs,with a focus on their main synthetic approaches,applications,and the advantages brought forth by introducing hierarchy. 展开更多
关键词 Porous organic molecular materials HIERARCHY Hydrogen-bonded organic frameworks Porous cages FULLERENE
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Recent advances in protein conformation sampling by combining machine learning with molecular simulation
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作者 唐一鸣 杨中元 +7 位作者 姚逸飞 周运 谈圆 王子超 潘瞳 熊瑞 孙俊力 韦广红 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期80-87,共8页
The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with... The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins. 展开更多
关键词 machine learning molecular simulation protein conformational space enhanced sampling
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Electronic effects on radiation damage inα-iron:A molecular dynamics study
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作者 江林 李敏 +2 位作者 付宝勤 崔节超 侯氢 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期521-529,共9页
Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation dur... Iron(Fe)-based alloys,which have been widely used as structural materials in nuclear reactors,can significantly change their microstructure properties and macroscopic properties under high flux neutron irradiation during operation,thus,the problems associated with the safe operation of nuclear reactors have been put forward naturally.In this work,a molecular dynamics simulation approach combined with electronic effects is developed for investigating the primary radiation damage process inα-Fe.Specifically,the influence of electronic effects on the collision cascade in Fe is systematically evaluated based on two commonly used interatomic potentials for Fe.The simulation results reveal that both electronic stopping(ES)and electron-phonon coupling(EPC)can contribute to the decrease of the number of defects in the thermal spike phase.The application of ES reduces the number of residual defects after the cascade evolution,whereas EPC has a reverse effect.The introduction of electronic effects promotes the formation of the dispersive subcascade:ES significantly changes the geometry of the damaged region in the thermal spike phase,whereas EPC mainly reduces the extent of the damaged region.Furthermore,the incorporation of electronic effects effectively mitigates discrepancies in simulation outcomes when using different interatomic potentials. 展开更多
关键词 radiation damage electronic effects molecular dynamics simulation α-iron
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The chemical environment and structural ordering in liquid Mg-Y-Zn system:An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure
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作者 Tangpeng Ma Jin Wang +5 位作者 Kaiming Cheng Chengwei Zhan Jixue Zhou Jingyu Qin Guochen Zhao Xinfang Zhang 《Journal of Magnesium and Alloys》 SCIE EI CAS CSCD 2024年第2期815-824,共10页
In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular... In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation.In liquid Mg-rich Mg-Y alloys,the strong Mg-Y interaction is determined,which promotes the formation of fivefold symmetric local structure.For Mg-Zn alloys,the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure.Due to the coexistence of Y and Zn,the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy,and contributes to the clustering of Mg,Y,Zn launched from Zn.What is more,the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys.These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure,which provides a new insight into the formation mechanism of LPSO structure at atomic level. 展开更多
关键词 Mg-Y-Zn Chemical environment Structural ordering ab-initio molecular dynamics
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Morphological and Molecular Data Revealed One New Species of the Short-legged Toads Brachytarsophrys Tian and Hu,1983(Anura,Megophryidae)from Yunnan,China
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作者 Yanhong HE Renda AI +5 位作者 Junkai HUANG Xianqi LI Xiaolong LIU Junlin LAN Jinmin CHEN Zhiyong YUAN 《Asian Herpetological Research》 SCIE CSCD 2024年第1期22-30,共9页
A new species of the genus Brachytarsophrys,named Brachytarsophrys wenshanensis sp.nov.,has been identified in southeastern Yunnan,China.This new species can be readily distinguished from other known congeners by both... A new species of the genus Brachytarsophrys,named Brachytarsophrys wenshanensis sp.nov.,has been identified in southeastern Yunnan,China.This new species can be readily distinguished from other known congeners by both morphological criterion and molecular analysis of three mitochondrial gene segments:16S,COI,and Cytb.This classification is based on the following morphological characters:(1)medium body size(SVL 83.8–85.1 mm in two adult males);(2)enormous head,with head width nearly 1.2 times the length;(3)tongue pyriform,feebly notched;(4)non-meeting heels;(5)male lacking nuptial pad;(6)tibiotarsal articulation reaching angle of mouth when hindlimbs are extended forward alongside the body;(7)absence of outer metatarsal tubercle,inner metatarsal tubercle elliptic and approximately equal to first toe;(8)rudimentary toe webbing,webbing formula:Ⅰ(2–)–(2^(++))Ⅱ(2^(–))–(3^(++))Ⅲ(2^(½))–(4)Ⅳ(4^(+))–(2^(⅔))V;(9)lateral fringes narrow;(10)dermal ridge or glandular fold on dorsum absent;(11)pectoral glands distinct and irregular,femoral gland small.Our work increases the number of species within the genus Brachytarsophrys to 9. 展开更多
关键词 AMPHIBIANS molecular phylogeny species diversity taxonomy
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Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation
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作者 SUN Wenting HU Yangdong +5 位作者 ZHENG Jiahuan SUN Qichao Chen Xia DING Jiakun ZHANG Weitao WU Lianying 《Journal of Ocean University of China》 CAS CSCD 2024年第2期467-476,共10页
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... 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. 展开更多
关键词 molecular dynamics simulation interaction distance interaction time rate electrolyte aqueous solutions SOLUBILITY
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Ab initio nonadiabatic molecular dynamics study on spin–orbit coupling induced spin dynamics in ferromagnetic metals
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作者 朱万松 郑镇法 +1 位作者 郑奇靖 赵瑾 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第1期156-163,共8页
Understanding the photoexcitation induced spin dynamics in ferromagnetic metals is important for the design of photo-controlled ultrafast spintronic device.In this work,by the ab initio nonadiabatic molecular dynamics... Understanding the photoexcitation induced spin dynamics in ferromagnetic metals is important for the design of photo-controlled ultrafast spintronic device.In this work,by the ab initio nonadiabatic molecular dynamics simulation,we have studied the spin dynamics induced by spin–orbit coupling(SOC)in Co and Fe using both spin-diabatic and spin-adiabatic representations.In Co system,it is found that the Fermi surface(E_(F))is predominantly contributed by the spin-minority states.The SOC induced spin flip will occur for the photo-excited spin-majority electrons as they relax to the E_(F),and the spin-minority electrons tend to relax to the EFwith the same spin through the electron–phonon coupling(EPC).The reduction of spin-majority electrons and the increase of spin-minority electrons lead to demagnetization of Co within100 fs.By contrast,in Fe system,the E_(F) is dominated by the spin-majority states.In this case,the SOC induced spin flip occurs for the photo-excited spin-minority electrons,which leads to a magnetization enhancement.If we move the E_(F) of Fe to higher energy by 0.6eV,the E_(F) will be contributed by the spin-minority states and the demagnetization will be observed again.This work provides a new perspective for understanding the SOC induced spin dynamics mechanism in magnetic metal systems. 展开更多
关键词 nonadiabatic molecular dynamics spin dynamics spin–orbit coupling ferromagnetic metal
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Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects
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作者 Changlin Li Wei Yang +5 位作者 Qiang Gan Yajun Wang Lin Liang Wenbo Zhang Shuangfei Zhu Changgen Feng 《Defence Technology(防务技术)》 SCIE EI CAS CSCD 2024年第1期364-374,共11页
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-dinitro... 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. 展开更多
关键词 CL-20 co-crystals molecular dynamics simulation Reactive forcefield Impact response Hot spot Void defect
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Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations
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作者 Xinyu Zhang Wenjie Xia +2 位作者 Yang Wang Liang Wang Xiaofeng Liu 《Computer Modeling in Engineering & Sciences》 SCIE EI 2024年第6期3047-3061,共15页
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 projectil... 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. 展开更多
关键词 Graphene aerogel molecular dynamics simulation impact response energy absorption
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