Molecular Simulations of Complex Membrane Models

Author(s):  
D. Jefferies ◽  
S. Khalid
2019 ◽  
Vol 252 (6) ◽  
pp. 627-638 ◽  
Author(s):  
Elisabeth Mantil ◽  
Iryna Buznytska ◽  
Grace Daly ◽  
Anatoli Ianoul ◽  
Tyler J. Avis

2018 ◽  
Vol 20 (47) ◽  
pp. 29764-29777 ◽  
Author(s):  
Carlos M. N. Mendonça ◽  
Debora T. Balogh ◽  
Simone C. Barbosa ◽  
Tânia E. Sintra ◽  
Sónia P. M. Ventura ◽  
...  

IL–phospholipid interactions were studied using Langmuir monolayers and molecular simulations.


2021 ◽  
Vol 6 (1) ◽  
pp. 1932589
Author(s):  
Mahmoud Moqadam ◽  
Thibault Tubiana ◽  
Emmanuel E. Moutoussamy ◽  
Nathalie Reuter

Biochimie ◽  
2016 ◽  
Vol 120 ◽  
pp. 105-109 ◽  
Author(s):  
David Shorthouse ◽  
George Hedger ◽  
Heidi Koldsø ◽  
Mark S.P. Sansom

Author(s):  
Brian Burke

The nuclear envelope is a complex membrane structure that forms the boundary of the nuclear compartment in eukaryotes. It regulates the passage of macromolecules between the two compartments and may be important for organizing interphase chromosome architecture. In interphase animal cells it forms a remarkably stable structure consisting of a double membrane ouerlying a protein meshwork or lamina and penetrated by nuclear pore complexes. The latter form the channels for nucleocytoplasmic exchange of macromolecules, At the onset of mitosis, however, it rapidly disassembles, the membranes fragment to yield small vesicles and the lamina, which is composed of predominantly three polypeptides, lamins R, B and C (MW approx. 74, 68 and 65 kDa respectiuely), breaks down. Lamins B and C are dispersed as monomers throughout the mitotic cytoplasm, while lamin B remains associated with the nuclear membrane vesicles.


2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>


2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak

<div> <div> <div> <p>In the present work we have investigated the possibility of using the Quantum Thermal Bath (QTB) method in molecular simulations of unimolecular dissociation processes. Notably, QTB is aimed in introducing quantum nuclear effects with a com- putational time which is basically the same as in newtonian simulations. At this end we have considered the model fragmentation of CH4 for which an analytical function is present in the literature. Moreover, based on the same model a microcanonical algorithm which monitor zero-point energy of products, and eventually modifies tra- jectories, was recently proposed. We have thus compared classical and quantum rate constant with these different models. QTB seems to correctly reproduce some quantum features, in particular the difference between classical and quantum activation energies, making it a promising method to study unimolecular fragmentation of much complex systems with molecular simulations. The role of QTB thermostat on rotational degrees of freedom is also analyzed and discussed. </p> </div> </div> </div>


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