Merging Experimental Evidence and Molecular Dynamics Theory to Develop Efficient Models of Solids Fracture

2016 ◽  
pp. 81-100
Author(s):  
C. A. Sciammarella ◽  
F. M. Sciammarella ◽  
L. Lamberti
Keyword(s):  
Molecular Dynamics ◽  
Experimental Evidence

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

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.

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

How do memory modules differentially contribute to familiarity and recollection?

2019 ◽  
Vol 42 ◽  
Author(s):  
Olya Hakobyan ◽  
Sen Cheng
Keyword(s):  
Recognition Memory ◽  
Experimental Evidence ◽  
Subjective Experience ◽  
Target Article ◽  
Memory Modules ◽  
Familiarity And Recollection ◽  
Memory Contents

Abstract We fully support dissociating the subjective experience from the memory contents in recognition memory, as Bastin et al. posit in the target article. However, having two generic memory modules with qualitatively different functions is not mandatory and is in fact inconsistent with experimental evidence. We propose that quantitative differences in the properties of the memory modules can account for the apparent dissociation of recollection and familiarity along anatomical lines.

Redox Reactions in Lipid Membranes as a Model for Primordial Energy-Conserving Systems

1997 ◽  
Vol 161 ◽  
pp. 437-442
Author(s):  
Salvatore Di Bernardo ◽  
Romana Fato ◽  
Giorgio Lenaz
Keyword(s):  
Experimental Evidence ◽  
Lipid Membranes ◽  
Energy Supply ◽  
Redox Reactions ◽  
Living Systems ◽  
Asymmetric Distribution ◽  
Conservation Of Energy ◽  
Asymmetrical Distribution ◽  
Energy Conserving ◽  
Living Organisms

AbstractOne of the peculiar aspects of living systems is the production and conservation of energy. This aspect is provided by specialized organelles, such as the mitochondria and chloroplasts, in developed living organisms. In primordial systems lacking specialized enzymatic complexes the energy supply was probably bound to the generation and maintenance of an asymmetric distribution of charged molecules in compartmentalized systems. On the basis of experimental evidence, we suggest that lipophilic quinones were involved in the generation of this asymmetrical distribution of charges through vectorial redox reactions across lipid membranes.

A Method for Setting the Clearance Angle

1972 ◽  
Vol 30 ◽  
pp. 388-389
Author(s):  
Michael T. Bucek ◽  
Howard J. Arnott
Keyword(s):  
Experimental Evidence ◽  
Light Source ◽  
Black Spot ◽  
Critical Factor ◽  
Clearance Angle ◽  
Crude Approximation ◽  
Ultrathin Sections

It is believed by the authors, with supporting experimental evidence, that as little as 0.5°, or less, knife clearance angle may be a critical factor in obtaining optimum quality ultrathin sections. The degree increments located on the knife holder provides the investigator with only a crude approximation of the angle at which the holder is set. With the increments displayed on the holder one cannot set the clearance angle precisely and reproducibly. The ability to routinely set this angle precisely and without difficulty would obviously be of great assistance to the operator. A device has been contrived to aid the investigator in precisely setting the clearance angle. This device is relatively simple and is easily constructed. It consists of a light source and an optically flat, front surfaced mirror with a minute black spot in the center. The mirror is affixed to the knife by placing it permanently on top of the knife holder.

Introductory Remarks

1980 ◽  
Vol 38 ◽  
pp. 598-599
Author(s):  
H. Mohri
Keyword(s):  
Muscle Contraction ◽  
Experimental Evidence ◽  
Sea Urchin ◽  
Constant Length ◽  
Thin Filaments ◽  
Bridge Formation ◽  
Thick Filaments ◽  
Sliding Mechanism ◽  
Radial Spokes ◽  
Cilia And Flagella

In 1959, Afzelius observed the presence of two rows of arms projecting from each outer doublet microtubule of the so-called 9 + 2 pattern of cilia and flagella, and suggested a possibility that the outer doublet microtubules slide with respect to each other with the aid of these arms during ciliary and flagellar movement. The identification of the arms as an ATPase, dynein, by Gibbons (1963)strengthened this hypothesis, since the ATPase-bearing heads of myosin molecules projecting from the thick filaments pull the thin filaments by cross-bridge formation during muscle contraction. The first experimental evidence for the sliding mechanism in cilia and flagella was obtained by examining the tip patterns of molluscan gill cilia by Satir (1965) who observed constant length of the microtubules during ciliary bending. Further evidence for the sliding-tubule mechanism was given by Summers and Gibbons (1971), using trypsin-treated axonemal fragments of sea urchin spermatozoa. Upon the addition of ATP, the outer doublets telescoped out from these fragments and the total length reached up to seven or more times that of the original fragment. Thus, the arms on a certain doublet microtubule can walk along the adjacent doublet when the doublet microtubules are disconnected by digestion of the interdoublet links which connect them with each other, or the radial spokes which connect them with the central pair-central sheath complex as illustrated in Fig. 1. On the basis of these pioneer works, the sliding-tubule mechanism has been established as one of the basic mechanisms for ciliary and flagellar movement.

Experimental evidence on the band structure of germanium and silicon

Physica ◽  
1954 ◽  
Vol 3 (7-12) ◽  
pp. 829-833
Author(s):  
C KITTEL
Keyword(s):  
Band Structure ◽  
Experimental Evidence
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