Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Hisashi Okumura ◽  
Satoru G. Itoh ◽  
Kazuhiro Nakamura ◽  
Takayasu Kawasaki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Nonequilibrium Molecular Dynamics ◽  
Water Molecules ◽  
Helix Structure ◽  
Dynamics Simulations ◽  
Structure Stabilization

scholarly journals New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 732
Author(s):  
Giovanni Bolcato ◽  
Maicol Bissaro ◽  
Giuseppe Deganutti ◽  
Mattia Sturlese ◽  
Stefano Moro
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Adenosine Receptors ◽  
Water Molecules ◽  
Primary Interest ◽  
Receptor Antagonists ◽  
Dynamics Simulations ◽  
Structural Insights

Adenosine receptors (ARs), like many otherGprotein-coupledreceptors (GPCRs), are targets of primary interest indrug design. However, one of the main limits for the development of drugs for this class of GPCRs is the complex selectivity profile usually displayed by ligands. Numerous efforts have been madefor clarifying the selectivity of ARs, leading to the development of many ligand-based models. The structure of the AR subtype A1 (A1AR) has been recently solved, providing important structural insights. In the present work, we rationalized the selectivity profile of two selective A1AR and A2AAR antagonists, investigating their recognition trajectories obtained by Supervised Molecular Dynamics from an unbound state and monitoring the role of the water molecules in the binding site.

scholarly journals Fluctuation Relations for Dissipative Systems in Constant External Magnetic Field: Theory and Molecular Dynamics Simulations

Entropy ◽  
2021 ◽  
Vol 23 (2) ◽  
pp. 146
Author(s):  
Alessandro Coretti ◽  
Lamberto Rondoni ◽  
Sara Bonella
Keyword(s):  
Magnetic Field ◽  
Molecular Dynamics ◽  
External Magnetic Field ◽  
Molecular Dynamics Simulations ◽  
Nonequilibrium Molecular Dynamics ◽  
Dissipative Systems ◽  
Common Belief ◽  
Fluctuation Relations ◽  
Dynamics Simulations ◽  
Constant External Magnetic Field

We illustrate how, contrary to common belief, transient Fluctuation Relations (FRs) for systems in constant external magnetic field hold without the inversion of the field. Building on previous work providing generalized time-reversal symmetries for systems in parallel external magnetic and electric fields, we observe that the standard proof of these important nonequilibrium properties can be fully reinstated in the presence of net dissipation. This generalizes recent results for the FRs in orthogonal fields—an interesting but less commonly investigated geometry—and enables direct comparison with existing literature. We also present for the first time a numerical demonstration of the validity of the transient FRs with nonzero magnetic field via nonequilibrium molecular dynamics simulations of a realistic model of liquid NaCl.

Exploring secondary interactions and the role of temperature in moisture-contaminated polymer networks through molecular simulations

Soft Matter ◽  
2021 ◽  
Vol 17 (10) ◽  
pp. 2942-2956
Author(s):  
Rishabh D. Guha ◽  
Ogheneovo Idolor ◽  
Katherine Berkowitz ◽  
Melissa Pasquinelli ◽  
Landon R. Grace
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Temperature Variation ◽  
Polymer Networks ◽  
Molecular Simulations ◽  
Effect Of Temperature ◽  
Secondary Interactions ◽  
Dynamics Simulations ◽  
Secondary Bonding

We investigated the effect of temperature variation on the secondary bonding interactions between absorbed moisture and epoxies with different morphologies using molecular dynamics simulations.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

2021 ◽  
Vol 23 (10) ◽  
pp. 5984-5991
Author(s):  
Letizia Tavagnacco ◽  
Ester Chiessi ◽  
Emanuela Zaccarelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Chain ◽  
Linear Polymer ◽  
Dynamics Simulations ◽  
Linear Polymer Chain

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we unveil the role of pressure in the coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM).

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