Osmotic ensemble methods for predicting adsorption-induced structural transitions in nanoporous materials using molecular simulations

2011 ◽  
Vol 134 (18) ◽  
pp. 184103 ◽  
Author(s):  
Ji Zang ◽  
Sankar Nair ◽  
David S. Sholl
Keyword(s):  
Molecular Simulations ◽  
Ensemble Methods ◽  
Nanoporous Materials ◽  
Structural Transitions

scholarly journals Histone tails cooperate to control the breathing of genomic nucleosomes

2020 ◽  
Author(s):  
Jan Huertas ◽  
Hans R Schöler ◽  
Vlad Cojocaru
Keyword(s):  
Epigenetic Regulation ◽  
Genomic Dna ◽  
Histone H3 ◽  
Molecular Simulations ◽  
Dna Interaction ◽  
Structural Transitions ◽  
Histone Tail ◽  
Chemical Modifications ◽  
Histone Tails ◽  
Chromatin Dynamics

Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 146 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and internucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 18μs. Transitions between open and closed nucleosome conformations were driven by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics.

Molecular Simulations of Adsorption and Diffusion in Crystalline Nanoporous Materials

2020 ◽  
pp. 199-319
Author(s):  
David Dubbeldam ◽  
Sofia Calero ◽  
Thijs J.H. Vlugt ◽  
Randall Q. Snurr
Keyword(s):  
Molecular Simulations ◽  
Nanoporous Materials ◽  
And Diffusion

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<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>

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulations

2019 ◽  
Author(s):  
Riccardo Spezia ◽  
Hichem Dammak
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Simulations ◽  
Zero Point ◽  
Thermal Bath ◽  
Unimolecular Dissociation ◽  
Point Energy ◽  
Rotational Degrees Of Freedom ◽  
The Difference ◽  
Nuclear Effects

<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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