Molecular dynamics prediction and experimental evidence for density of normal and metastable liquid zirconium

2016 ◽  
Vol 653 ◽  
pp. 112-116 ◽  
Author(s):  
H.P. Wang ◽  
S.J. Yang ◽  
L. Hu ◽  
B. Wei
Keyword(s):  
Molecular Dynamics ◽  
Experimental Evidence ◽  
Metastable Liquid

Molecular Dynamics Studies of Defects in Si

1990 ◽  
Vol 209 ◽  
Author(s):  
M.S. Duesbery ◽  
D.J. Michel ◽  
Efthimios Kaxiras ◽  
B. Joos
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamic Simulation ◽  
Experimental Evidence ◽  
Dynamic Simulation ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Recent Literature ◽  
Empirical Potentials ◽  
Generalized Stacking Fault ◽  
Generalized Stacking Fault Energy

ABSTRACTThe efficacy of three modern empirical potentials in the molecular dynamic simulation of the configurations, energies and mobility of dislocation cores and their excitations is assessed in the light of recent literature. The results are found to be inconsistent both between different potentials and with experimental evidence. It is argued that the discrepancies are rooted in the limited databases which have been used in the construction of empirical potentials. The reason for the discrepancies is demonstrated by comparing empirical and density functional calculations of the generalized stacking fault energy.

scholarly journals Embelin inhibits TNF-α converting enzyme and cancer cell metastasis: molecular dynamics and experimental evidence

BMC Cancer ◽  
2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Jaspreet Kaur Dhanjal ◽  
Nupur Nigam ◽  
Sudhanshu Sharma ◽  
Anupama Chaudhary ◽  
Sunil C Kaul ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Experimental Evidence ◽  
Cancer Cell ◽  
Converting Enzyme ◽  
Cell Metastasis ◽  
Tnf Α

Molecular dynamics prediction of density for metastable liquid noble metals

2012 ◽  
Vol 539-540 ◽  
pp. 30-34 ◽  
Author(s):  
H.P. Wang ◽  
S.J. Yang ◽  
B. Wei
Keyword(s):  
Molecular Dynamics ◽  
Noble Metals ◽  
Metastable Liquid

scholarly journals Molecular Mechanism of Gelsemium elegans (Gardner and Champ.) Benth. Against Neuropathic Pain Based on Network Pharmacology and Experimental Evidence

2022 ◽  
Vol 12 ◽  
Author(s):  
Wancai Que ◽  
Zhaoyang Wu ◽  
Maohua Chen ◽  
Binqing Zhang ◽  
Chuihuai You ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neuropathic Pain ◽  
Molecular Dynamics Simulation ◽  
Experimental Evidence ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Dynamics Simulation ◽  
Network Pharmacology ◽  
Holistic View

Gelsemium elegans (Gardner and Champ.) Benth. (Gelsemiaceae) (GEB) is a toxic plant indigenous to Southeast Asia especially China, and has long been used as Chinese folk medicine for the treatment of various types of pain, including neuropathic pain (NPP). Nevertheless, limited data are available on the understanding of the interactions between ingredients-targets-pathways. The present study integrated network pharmacology and experimental evidence to decipher molecular mechanisms of GEB against NPP. The candidate ingredients of GEB were collected from the published literature and online databases. Potentially active targets of GEB were predicted using the SwissTargetPrediction database. NPP-associated targets were retrieved from GeneCards, Therapeutic Target database, and DrugBank. Then the protein-protein interaction network was constructed. The DAVID database was applied to Gene Ontology and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Molecular docking was employed to validate the interaction between ingredients and targets. Subsequently, a 50 ns molecular dynamics simulation was performed to analyze the conformational stability of the protein-ligand complex. Furthermore, the potential anti-NPP mechanisms of GEB were evaluated in the rat chronic constriction injury model. A total of 47 alkaloids and 52 core targets were successfully identified for GEB in the treatment of NPP. Functional enrichment analysis showed that GEB was mainly involved in phosphorylation reactions and nitric oxide synthesis processes. It also participated in 73 pathways in the pathogenesis of NPP, including the neuroactive ligand-receptor interaction signaling pathway, calcium signaling pathway, and MAPK signaling pathway. Interestingly, 11-Hydroxyrankinidin well matched the active pockets of crucial targets, such as EGFR, JAK1, and AKT1. The 11-hydroxyrankinidin-EGFR complex was stable throughout the entire molecular dynamics simulation. Besides, the expression of EGFR and JAK1 could be regulated by koumine to achieve the anti-NPP action. These findings revealed the complex network relationship of GEB in the “multi-ingredient, multi-target, multi-pathway” mode, and explained the synergistic regulatory effect of each complex ingredient of GEB based on the holistic view of traditional Chinese medicine. The present study would provide a scientific approach and strategy for further studies of GEB in the treatment of NPP in the future.

scholarly journals Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
G. Zhao ◽  
J. L. Yan ◽  
Y. J. Yu ◽  
M. C. Ding ◽  
X. G. Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Liquid Silicon ◽  
Ab Initio Molecular Dynamics ◽  
Metastable Liquid ◽  
Structural Order

Rationalizing the Design of Hyaluronic Acid-Decorated Liposomes for Targeting Epidermal Layers: A Combination of Molecular Dynamics and Experimental Evidence

2021 ◽  
Author(s):  
Silvia Franzé ◽  
Francesco Rama ◽  
Paolo Rocco ◽  
Michela Debernardi ◽  
Valeria Bincoletto ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hyaluronic Acid ◽  
Experimental Evidence
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