Direct All-Atom Molecular Dynamics Simulations of the Effects of Short Chain Branching on Polyethylene Oligomer Crystal Nucleation

2018 ◽  
Vol 51 (13) ◽  
pp. 4762-4769 ◽  
Author(s):  
Wenlin Zhang ◽  
Ronald G. Larson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Nucleation ◽  
Short Chain ◽  
Chain Branching ◽  
Dynamics Simulations

Conformational and aggregation properties of PffBT4T polymers: atomistic insight into the impact of alkyl-chain branching positions

2019 ◽  
Vol 7 (45) ◽  
pp. 14198-14204
Author(s):  
Lu Ning ◽  
Guangchao Han ◽  
Yuanping Yi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Alkyl Chain ◽  
Temperature Dependent ◽  
Chain Branching ◽  
Alkyl Chains ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

The impact of the branching positions of alkyl chains on temperature dependent aggregation is rationalized by atomistic molecular dynamics simulations.

Nucleation of pseudo hard-spheres and dumbbells at moderate metastability: appearance of A15 Frank–Kasper phase at intermediate elongations

2019 ◽  
Vol 21 (4) ◽  
pp. 1656-1670 ◽  
Author(s):  
Itziar Zubieta ◽  
Miguel Vázquez del Saz ◽  
Pablo Llombart ◽  
Carlos Vega ◽  
Eva G. Noya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hard Spheres ◽  
Crystal Nucleation ◽  
Brute Force ◽  
Dynamics Simulations

Crystal nucleation of repulsive hard-dumbbells from the sphere to the two tangent spheres limit is investigated at moderately high metastability by brute-force molecular dynamics simulations.

scholarly journals Structural and Kinetic Insights Into the Molecular Basis of Salt Tolerance of the Short-Chain Glucose-6-Phosphate Dehydrogenase From Haloferax volcanii

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolás Fuentes-Ugarte ◽  
Sixto M. Herrera ◽  
Pablo Maturana ◽  
Victor Castro-Fernandez ◽  
Victoria Guixé
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Characteristics ◽  
Conformational Dynamics ◽  
High Salt ◽  
Haloferax Volcanii ◽  
Short Chain ◽  
Dynamics Simulations ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Promising Source

Halophilic enzymes need high salt concentrations for activity and stability and are considered a promising source for biotechnological applications. The model study for haloadaptation has been proteins from the Halobacteria class of Archaea, where common structural characteristics have been found. However, the effect of salt on enzyme function and conformational dynamics has been much less explored. Here we report the structural and kinetic characteristics of glucose-6-phosphate dehydrogenase from Haloferax volcanii (HvG6PDH) belonging to the short-chain dehydrogenases/reductases (SDR) superfamily. The enzyme was expressed in Escherichia coli and successfully solubilized and refolded from inclusion bodies. The enzyme is active in the presence of several salts, though the maximum activity is achieved in the presence of KCl, mainly by an increment in the kcat value, that correlates with a diminution of its flexibility according to molecular dynamics simulations. The high KM for glucose-6-phosphate and its promiscuous activity for glucose restrict the use of HvG6PDH as an auxiliary enzyme for the determination of halophilic glucokinase activity. Phylogenetic analysis indicates that SDR-G6PDH enzymes are exclusively present in Halobacteria, with HvG6PDH being the only enzyme characterized. Homology modeling and molecular dynamics simulations of HvG6PDH identified a conserved NLTX2H motif involved in glucose-6-phosphate interaction at high salt concentrations, whose residues could be crucial for substrate specificity. Structural differences in its conformational dynamics, potentially related to the haloadaptation strategy, were also determined.

Nanocontraction flows of short-chain polyethylene via molecular dynamics simulations

2009 ◽  
Vol 35 (8) ◽  
pp. 691-704 ◽  
Author(s):  
Huan-Chang Tseng ◽  
Jiann-Shing Wu ◽  
Rong-Yeu Chang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Chain ◽  
Dynamics Simulations
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