nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions
Vania Calandrini,E. Pellegrini,Paolo Calligari,Konrad Hinsen,Gerald R. Kneller,Gerald R. Kneller +5 more
- Vol. 12, pp 201-232
TLDR
A synoptic view of the range of applications of the latest version of nMoldyn is presented, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infraredSpectroscopy and for protein secondary structure analysis.Abstract:
This article gives an introduction into the program nMoldyn, which has been originally conceived to support the interpretation of neutron scattering experiments on complex molecular systems by the calculation of appropriate time correlation functions from classical and quantum molecular dynamics simulations of corresponding model systems. Later the functionality has been extended to include more advanced time series analyses of molecular dynamics trajectories, in particular the calculation of memory functions, which play an essential role in the theory of time correlation functions. Here we present a synoptic view of the range of applications of the latest version of nMoldyn, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infrared spectroscopy and for protein secondary structure analysis.read more
Citations
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Hydrodynamics of Diffusion in Lipid Membrane Simulations.
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Thermophysical properties of glyceline–water mixtures investigated by molecular modelling
TL;DR: The combined application of PC-SAFT to efficiently predict static properties and molecular dynamics simulations to predict static and dynamic properties offers a powerful framework in solvent design applications.
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Cancer cells in the tumor core exhibit spatially coordinated migration patterns
Ralitza Staneva,Ralitza Staneva,Fatima El Marjou,Jorge Barbazan,Denis Krndija,Sophie Richon,Andrew G. Clark,Danijela Matic Vignjevic +7 more
TL;DR: Tissue explant imaging reveals that cancer cells in the tumor core migrate in a coordinated manner that is actively driven by the actin cytoskeleton.
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Combination of Inelastic Neutron Scattering Experiments and ab Initio Quantum Calculations for the Study of the Hydration Properties of Oriented Saponites
Mónica Jiménez-Ruiz,Eric Ferrage,Marc Blanchard,Javier Fernandez-Castanon,Alfred Delville,M. R. Johnson,Laurent J. Michot +6 more
TL;DR: In this article, the authors study the hydration of synthetic saponite clay samples by combining inelastic neutron scattering (INS) experiments and ab initio quantum calculations, that include normal modes analysis and ab- initio molecular dynamics simulations (AIMD).
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Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations
TL;DR: Molecular dynamics simulations of the protein adenine nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid membranes show that the hydrodynamic finite-size correction for rotational diffusion is accurate in standard-use cases.
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