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Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

ABSTRACT: The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160?000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

SUBMITTER: Glowacki DR

PROVIDER: S-EPMC5360904 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

Glowacki David R DR Rodgers W J WJ Shannon Robin R Robertson Struan H SH Harvey Jeremy N JN

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 20170401 2092

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'ho ...[more]

PMID: 28320908

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Project description:BackgroundThe concentration gradient of Bicoid protein which determines the developmental pathways in early Drosophila embryo is the best characterized morphogen gradient at the molecular level. Because different developmental fates can be elicited by different concentrations of Bicoid, it is important to probe the limits of this specification by analyzing intrinsic fluctuations of the Bicoid gradient arising from small molecular number. Stochastic simulations can be applied to further the understanding of the dynamics of Bicoid morphogen gradient formation at the molecular number level, and determine the source of the nucleus-to-nucleus expression variation (noise) observed in the Bicoid gradient.ResultsWe compared quantitative observations of Bicoid levels in immunostained Drosophila embryos with a spatially extended Master Equation model which represents diffusion, decay, and anterior synthesis. We show that the intrinsic noise of an autonomous reaction-diffusion gradient is Poisson distributed. We demonstrate how experimental noise can be identified in the logarithm domain from single embryo analysis, and then separated from intrinsic noise in the normalized variance domain of an ensemble statistical analysis. We show how measurement sensitivity affects our observations, and how small amounts of rescaling noise can perturb the noise strength (Fano factor) observed. We demonstrate that the biological noise level in data can serve as a physical constraint for restricting the model's parameter space, and for predicting the Bicoid molecular number and variation range. An estimate based on a low variance ensemble of embryos suggests that the steady-state Bicoid molecular number in a nucleus should be larger than 300 in the middle of the embryo, and hence the gradient should extend to the posterior end of the embryo, beyond the previously assumed background limit. We exhibit the predicted molecular number gradient together with measurement effects, and make a comparison between conditions of higher and lower variance respectively.ConclusionQuantitative comparison of Master Equation simulations with immunostained data enabled us to determine narrow ranges for key biophysical parameters, which for this system can be independently validated. Intrinsic noise is clearly detectable as well, although the staining process introduces certain limits in resolution.

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Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

Publications

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

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