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Register a new userMolecular dynamics simulation of nanocolloidal amorphous silica particles: Part I
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Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, of diameter 4.4 nm with four different background electrolyte concentrations, to extract the mean force acting between the pair of silica nanoparticles. Dependences of the interparticle forces with separation and the background electrolyte concentration were demonstrated. The nature of the interaction of the counter-ions with charged silica surface sites (deprotonated silanols) was investigated. A patchy double layer of adsorbed sodium counter-ions. was observed. Dependences of the interparticle potential of mean force with separation and the background electrolyte concentration were demonstrated. Direct evidence of the solvation forces is presented in terms of changes of the water ordering at the surfaces of the isolated and double nanoparticles. The nature of the interaction of the counter-ions with charged silica surface sites (deprotonated silanols) was investigated in terms of quantifying the effects of the number of water molecules separately inside each of the pair of nanoparticles by defining an impermeability measure. A direct correlation was found between impermeability (related to the silica surface hairiness) and the disruption of water ordering. Differences in the impermeability between the two nanoparticles are attributed to differences in the calculated electric dipole moment.
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Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four different background electrolyte concentrations. Dependence of the inter-particle potential of mean force on the separation and the silicon to sodium ratio, as well as on the background electrolyte concentration, are demonstrated. The pH was indirectly accounted for via the ratio of silicon to sodium used in the simulations. The nature of the interaction of the counter-ions with charged silica surface sites (deprotonated silanols) was also investigated. The effect of the sodium double layer on the water ordering was investigated for three Si:Na+ ratios. The number of water molecules trapped inside the nanoparticles was investigated as the Si:Na+ ratio was varied. Differences in this number between the two nanoparticles in the simulations are attributed to differences in the calculated electric dipole moment. The implications of the form of the potentials for aggregation are also discussed.
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK potential, that has been recently proposed by Carre et al. The experimental equation of state is well-reproduced by the CHIK model. With increasing pressure (density), the structure changes from a tetrahedral network to a network containing a high number of five- and six-fold Si-O coordination. In the partial static structure factors, this change of the structure with increasing density is reflected by a shift of the first sharp diffraction peak towards higher wavenumbers q, eventually merging with the main peak at densities around 4.2 g/cm^3. The self-diffusion constants as a function of pressure show the experimentally-known maximum, occurring around a pressure of about 20 GPa.
The dynamics of a molecule in a magnetic field is significantly different form its zero-field counterpart. One important difference in the presence of a field is the Lorentz force acting on the nuclei, which can be decomposed as the sum of the bare nuclear Lorentz force and a screening force due to the electrons. This screening force is calculated from the Berry curvature and can change the dynamics qualitatively. It is therefore important to include the contributions from the Berry curvature in molecular dynamics simulations in a magnetic field. In this work, we present a scheme for calculating the Berry curvature numerically, by a finite-difference technique, addressing challenges related to the arbitrary global phase of the wave function. The Berry curvature is calculated as a function of bond distance for H$_2$ at the restricted and unrestricted Hartree--Fock levels of theory and for CH$^{+}$ as a function of the magnetic field strength at the restricted Hartree--Fock level of theory. The calculations are carried out using basis sets of contracted Gaussian functions equipped with London phase factors (London orbitals) to ensure gauge-origin invariance. In the paper, we also interpret the Berry curvature in terms of atomic charges and discuss its convergence in basis sets with and without London phase factors. Calculation of the Berry curvature allows for its inclusion in textit{ab initio} molecular dynamics simulations in a magnetic field.
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.
By using molecular dynamics simulation, formation mechanisms of amorphous carbon in particular sp${}^3$ rich structure was researched. The problem that reactive empirical bond order potential cannot represent amorphous carbon properly was cleared in the transition process from graphite to diamond by high pressure and the deposition process of amorphous carbon thin films. Moreover, the new potential model which is based on electron distribution simplified as a point charge was developed by using downfolding method. As a result, the molecular dynamics simulation with the new potential could demonstrate the transition from graphite to diamond at the pressure of 15 GPa corresponding to experiment and the deposition of sp${}^3$ rich amorphous carbon.
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