scholarly journals Molecular Dynamics of Janus Nanodimers Dispersed in Lamellar Phases of a Block Copolymer

Polymers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1524
Author(s):  
J. Javier Burgos-Mármol ◽  
Alessandro Patti
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Lamellar Spacing ◽  
Space Distribution ◽  
Time Dynamics ◽  
Excluded Volume Effects ◽  
Lamellar Phases ◽  
Guest Species ◽  
Long Time ◽  
Dynamics Simulations

We investigate structural and dynamical properties of Janus nanodimers (NDs) dispersed in lamellar phases of a diblock copolymer. By performing molecular dynamics simulations, we show that an accurate tuning of the interactions between NDs and copolymer blocks can lead to a close control of NDs’ space distribution and orientation. In particular, NDs are preferentially found within the lamellae if enthalpy-driven forces offset their entropic counterpart. By contrast, when enthalpy-driven forces are not significant, the distribution of NDs, preferentially observed within the inter-lamellar spacing, is mostly driven by excluded-volume effects. Not only does the degree of affinity between host and guest species drive the NDs’ distribution in the polymer matrix, but it also determines their space orientation. In turn, these key structural properties influence the long-time dynamics and the ability of NDs to diffuse through the polymer matrix.

scholarly journals Study of the Lamellar and Micellar Phases of Pluronic F127: A Molecular Dynamics Approach

Processes ◽  
2019 ◽  
Vol 7 (9) ◽  
pp. 606 ◽  
Author(s):  
Juan Albano ◽  
Damian Grillo ◽  
Julio Facelli ◽  
Marta Ferraro ◽  
Mónica Pickholz
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Structure ◽  
Pluronic F127 ◽  
Coarse Grain ◽  
Lamellar Thickness ◽  
Initial Polymer ◽  
Lamellar Phases ◽  
New Information ◽  
Order Of Magnitude ◽  
Dynamics Simulations

In this work, we analyzed the behavior of Pluronic F127 through molecular dynamics simulations at the coarse-grain level, focusing on the micellar and lamellar phases. To this aim, two initial polymer conformations were considered, S-shape and U-shape, for both simulated phases. Through the simulations, we were able to examine the structural and mechanical properties that are difficult to access through experiments. Since no transition between S and U shapes was observed in our simulations, we inferred that all single co-polymers had memory of their initial configuration. Nevertheless, most copolymers had a more complex amorphous structure, where hydrophilic beads were part of the lamellar-like core. Finally, an overall comparison of the micellar a lamellar phases showed that the lamellar thickness was in the same order of magnitude as the micelle diameter (approx. 30 nm). Therefore, high micelle concentration could lead to lamellar formation. With this new information, we could understand lamellae as orderly packed micelles.

scholarly journals ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

2014 ◽  
Vol 169 ◽  
pp. 119-142 ◽  
Author(s):  
Matthieu Dreher ◽  
Jessica Prevoteau-Jonquet ◽  
Mikael Trellet ◽  
Marc Piuzzi ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular System ◽  
Data Set ◽  
System P ◽  
Alternative Approach ◽  
Long Time ◽  
Flexible Framework ◽  
Sheer Size ◽  
Dynamics Simulations

The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long-time batch executions). During interactive sessions, at runtime, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a CAVE-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system.

scholarly journals Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

2014 ◽  
Vol 372 (2021) ◽  
pp. 20130384 ◽  
Author(s):  
Jonathan Booth ◽  
Saulo Vazquez ◽  
Emilio Martinez-Nunez ◽  
Alison Marks ◽  
Jeff Rodgers ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Unfolding ◽  
Integrated Approach ◽  
Potential Of Mean Force ◽  
Molecular Systems ◽  
Time Dynamics ◽  
Peptide Cyclization ◽  
Thermodynamics And Kinetics ◽  
Assembled Monolayers ◽  
Long Time

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

scholarly journals The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3424
Author(s):  
Hugo A. L. Filipe ◽  
Maria João Moreno ◽  
Luís M. S. Loura
Keyword(s):  
Molecular Dynamics ◽  
Membrane System ◽  
Md Simulations ◽  
Fluorescence Probes ◽  
Host Membrane ◽  
Tremendous Progress ◽  
Long Time ◽  
Experimental Approaches ◽  
Dynamics Simulations ◽  
Membrane Probes

Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.

scholarly journals Molecular dynamics of the histamine H3 membrane receptor reveals different mechanisms of GPCR signal transduction

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Leonardo David Herrera-Zúñiga ◽  
Liliana Marisol Moreno-Vargas ◽  
Luck Ballaud ◽  
José Correa-Basurto ◽  
Diego Prada-Gracia ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Signal Transduction ◽  
Complex Behavior ◽  
Dipalmitoyl Phosphatidyl Choline ◽  
Extensive Analysis ◽  
Long Time ◽  
Dynamics Simulations ◽  
G Protein Coupled ◽  
Gpcr Signal ◽  
Histamine H3

Abstract In this work, we studied the mechanisms of classical activation and inactivation of signal transduction by the histamine H3 receptor, a 7-helix transmembrane bundle G-Protein Coupled Receptor through long-time-scale atomistic molecular dynamics simulations of the receptor embedded in a hydrated double layer of dipalmitoyl phosphatidyl choline, a zwitterionic polysaturated ordered lipid. Three systems were prepared: the apo receptor, representing the constitutively active receptor; and two holo-receptors—the receptor coupled to the antagonist/inverse agonist ciproxifan, representing the inactive state of the receptor, and the receptor coupled to the endogenous agonist histamine and representing the active state of the receptor. An extensive analysis of the simulation showed that the three states of H3R present significant structural and dynamical differences as well as a complex behavior given that the measured properties interact in multiple and interdependent ways. In addition, the simulations described an unexpected escape of histamine from the orthosteric binding site, in agreement with the experimental modest affinities and rapid off-rates of agonists.

Fragmentation of KrN+ clusters after electron impact ionization II. Long-time dynamics simulations of Kr7+ evolution and the role of initial electronic excitation

2017 ◽  
Vol 19 (37) ◽  
pp. 25423-25440 ◽  
Author(s):  
Ivan Janeček ◽  
Martin Stachoň ◽  
Florent Xavier Gadea ◽  
René Kalus
Keyword(s):  
Electron Impact ◽  
Electronic Excitation ◽  
Impact Ionization ◽  
Electron Impact Ionization ◽  
Time Dynamics ◽  
Long Time ◽  
Dynamics Simulations ◽  
Long Time Dynamics

Long time simulations, up to 100 ns, have been performed for the fragmentation of Kr7+ clusters after electron impact ionization, and have been compared with experiment.

Dynamics of linear and branched alkane melts: Molecular dynamics test of theory for long time dynamics

1998 ◽  
Vol 108 (21) ◽  
pp. 9155-9167 ◽  
Author(s):  
Konstantin S. Kostov ◽  
Karl F. Freed ◽  
Edmund B. Webb ◽  
Maurizio Mondello ◽  
Gary S. Grest
Keyword(s):  
Molecular Dynamics ◽  
Time Dynamics ◽  
Long Time ◽  
Long Time Dynamics
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