Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 m s. The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.
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http://dx.doi.org/10.1039/c7sc02763j | DOI Listing |
Langmuir
January 2025
Department of Physics, K. N. Toosi University of Technology, Tehran 19697, Iran.
One of the successful techniques developed for the inhibition of metal corrosion is the utilization of phytochemicals from plant extracts as corrosion inhibitors. Theoretical studies are utilized to predict how organic components behave on metal surfaces and can pave the way for the development and synthesis of innovative, efficient corrosion inhibitors. However, atomic-level insights into the inhibition mechanisms of these green components are still needed.
View Article and Find Full Text PDFSoft Matter
January 2025
Computation-based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus.
This work presents an investigation of the influence of poly(-isopropylacrylamide) (PNIPAM) polymer on the structural dynamics of intrinsically disordered alpha-synuclein (α-syn) protein, exploring the formation and intricate features of the resulting α-syn/PNIPAM complexes. Using atomistic molecular dynamics (MD) simulations, our study analyzes the impact of initial configuration, polymer molecular weight, and protein mutations on the α-syn and the α-syn/PNIPAM complex. Atomistic simulations, of a few μs, of the protein/polymer complex reveal crucial insights into molecular interactions within the complex, emphasizing a delicate balance of forces governing its stability and structural evolution.
View Article and Find Full Text PDFThe big potassium (BK) channels remain open with a small limiting probability of ∼ 10 at minimal Ca and negative voltages < -100 mV. The molecular origin and functional significance of such "intrinsic opening" are not understood. Here we combine atomistic simulations and electrophysiological experiments to show that the intrinsic opening of BK channels is an inherent property of the vapor barrier, generated by hydrophobic dewetting of the BK inner pore in the deactivated state.
View Article and Find Full Text PDFAs more powerful high performance computing resources are becoming available, there is a new opportunity to bring the unique capabilities of molecular dynamics (MD) simulations to cell-scale systems. Membranes are ubiquitous within cells and are responsible for a diverse set of essential biological functions, but building atomistic models of cell-scale membranes for MD simulations is immensely challenging because of their vast sizes, complex geometries, and complex compositions. To meet this challenge, we have developed xMAS Builder (E perimentally-Derived embranes of rbitrary hape Builder), which is designed to take experimental lipidomics and structural (e.
View Article and Find Full Text PDFChem Sci
January 2025
Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge TN 37830 USA
The successful design and deployment of next-generation nuclear technologies heavily rely on thermodynamic data for relevant molten salt systems. However, the lack of accurate force fields and efficient methods has limited the quality of thermodynamic predictions from atomistic simulations. Here we propose an efficient free energy framework for computing chemical potentials, which is the central free energy quantity behind many thermodynamic properties.
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