Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userMolecular Simulation of Covalent Bond Dynamics in Liquid Silicon
398
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent non-trivial effects on liquid state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio simulation-based approach for quantifying the structure and dynamics of covalent bonds in condensed phases. Through the examination of structural correlations among silicon nuclei and maximally localized Wannier function centers, we develop a geometric criterion for covalent bonds in liquid Si. We use this to monitor the dynamics of transient covalent bonding in the liquid state and estimate a covalent bond lifetime. We compare covalent bond dynamics to other processes in liquid Si and similar liquids and suggest experiments to measure the covalent bond lifetime.
rate research
Read More
Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure calculations on isolated molecules and/or crystal structures that are not readily transferable to liquids and disordered phases. To address this issue, we present a first-principles simulation-based approach for quantifying halogen bonds in molecular systems rooted in an understanding of nuclei-nuclei and electron-nuclei spatial correlations. We then demonstrate how this approach can be used to quantify the structure and dynamics of halogen bonds in condensed phases, using solid and liquid molecular chlorine as prototypical examples with high concentrations of halogen bonds. We close with a discussion of how the knowledge generated by our first-principles approach may inform the development of classical empirical models, with a consistent representation of halogen bonding.
Traditional classifications of crystalline phases focus on nuclear degrees of freedom. Through examination of both electronic and nuclear structure, we introduce the concept of an electronic plastic crystal. Such a material is classified by crystalline nuclear structure, while localized electronic degrees of freedom - here lone pairs - exhibit orientational motion at finite temperatures. This orientational motion is an emergent phenomenon arising from the coupling between electronic structure and polarization fluctuations generated by collective motions, such as phonons. Using ab initio molecular dynamics simulations, we predict the existence of electronic plastic crystal motion in halogen crystals and halide perovskites, and suggest that such motion may be found in a broad range of solids with lone pair electrons. Such fluctuations in the charge density should be observable, in principle via synchrotron scattering.
The dynamics of desorption from a submonolayer of adsorbed atoms or ions are significantly influenced by the absence or presence of lateral diffusion of the adsorbed particles. When diffusion is present, the adsorbate configuration is simultaneously changed by two distinct processes, proceeding in parallel: adsorption/desorption, which changes the total adsorbate coverage, and lateral diffusion, which is coverage conserving. Inspired by experimental results, we here study the effects of these competing processes by kinetic Monte Carlo simulations of a simple lattice-gas model. In order to untangle the various effects, we perform large-scale simulations, in which we monitor coverage, correlation length, and cluster-size distributions, as well as the behavior of representative individual clusters, during desorption. For each initial adsorbate configuration, we perform multiple, independent simulations, without and with diffusion, respectively. We find that, compared to desorption without diffusion, the coverage-conserving diffusion process produces two competing effects: a retardation of the desorption rate, which is associated with a coarsening of the adsorbate configuration, and an acceleration due to desorption of monomers evaporated from the cluster perimeters. The balance between these two effects is governed by the structure of the adsorbate layer at the beginning of the desorption process. Deceleration and coarsening are predominant for configurations dominated by monomers and small clusters, while acceleration is predominant for configurations dominated by large clusters.
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.
The modelling of interface migration and the associated diffusion mechanisms at the nanoscale level is a challenging issue. For many technological applications ranging from nanoelectronic devices to solar cells, more knowledge of the mechanisms governing the migration of the silicon amorphous/crystalline interface and dopant diffusion during solid phase epitaxy is needed. In this work, silicon recrystallisation in the framework of solid phase epitaxy and the influence on orientation effects have been investigated at the atomic level using empirical molecular dynamics simulations. The morphology and the migration process of the interface has been observed to be highly dependent on the original inter-facial atomic structure. The [100] interface migration is a quasi-planar ideal process whereas the cases [110] and [111] are much more complex with a more diffuse interface. For [110], the interface migration corresponds to the formation and dissolution of nanofacets whereas for [111] a defective based bilayer reordering is the dominant re-growth process. The study of the interface velocity migration in the ideal case of defect free re-growth reveals no difference between [100] and [110] and a decrease by a mean factor of 1.43 for the case [111]. Finally, the influence of boron atoms in the amorphous part on the interface migration velocity is also investigated in the case of [100] orientation.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
