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Register a new userNew fitting scheme to obtain effective potential from Car-Parrinello molecular dynamics simulations: Application to silica
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A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing the transferability of the new potential.
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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.
A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries (RFB). Here, we employ Car-Parrinello molecular dynamics (CPMD) simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction and diffusion of aqueous V$^{2+}$, V$^{3+}$, VO$^{2+}$, and VO$_2^+$ ions at 300 K. The results indicate that the first hydration shell of both V$^{2+}$ and V$^{3+}$ contains six water molecules, while VO$^{2+}$ is coordinated to five and VO$_2^+$ to three water ligands. The first acidity constants (p$K_mathrm{a}$) estimated using metadynamics simulations are 2.47, 3.06 and 5.38 for aqueous V$^{3+}$, VO$_2^+$ and VO$^{2+}$, respectively, while V$^{2+}$ is predicted to be a fairly weak acid in aqueous solution with a p$K_mathrm{a}$ value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO$_2^+$ ion has a significant impact on water hydrolysis leading to a much higher p$K_mathrm{a}$ value of 4.8. This should result in a lower propensity of aqueous VO$_2^+$ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V$^{3+}$ $<$ VO$_2^+$ $<$ VO$^{2+}$ $<$ V$^{2+}$ and thus correlate with the simulated hydrolysis constants, namely, the higher the p$K_mathrm{a}$ value, the greater the diffusion coefficient.
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse grained MARTINI models and structure based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.
Using the potential energy landscape formalism we show that, in the temperature range in which the dynamics of a glass forming system is thermally activated, there exists a unique set of basis glass states each of which is confined to a single metabasin of the energy landscape of a glass forming system. These basis glass states tile the entire configuration space of the system, exhibit only secondary relaxation and are solid-like. Any macroscopic state of the system (whether liquid or glass) can be represented as a superposition of basis glass states and can be described by a probability distribution over these states. During cooling of a liquid from a high temperature, the probability distribution freezes at sufficiently low temperatures describing the process of liquid to glass transition. The time evolution of the probability distribution towards the equilibrium distribution during subsequent aging describes the primary relaxation of a glass.
We computer model a free-standing vitreous silica bilayer which has recently been synthesized and characterized experimentally in landmark work. Here we model the bilayer using a computer assembly procedure that starts from a single layer of amorphous graphene, generated using a bond switching algorithm from an initially crystalline graphene structure. Next each bond is decorated with an oxygen atom and the carbon atoms are relabeled as silicon. This monolayer can be now thought of as a two dimensional network of corner sharing triangles. Next each triangle is made into a tetrahedron, by raising the silicon atom above each triangle and adding an additional singly coordinated oxygen atom at the apex. The final step is to mirror reflect this layer to form a second layer and then attach the two layers together to form the bilayer. We show that this vitreous silica bilayer has the additional macroscopic degrees of freedom to easily form a network of identical corner sharing tetrahedra if there is a symmetry plane through the center of the bilayer going through the layer of oxygen ions that join the upper and lower layers. This has the consequence that the upper rings lie exactly above the lower rings, which are tilted in general. The assumption of a network of perfect corner sharing tetrahedra leads to a range of possible densities that we have previously characterized in three dimensional zeolites as a flexibility window. Finally, using a realistic potential, we have relaxed the bilayer to determine the density, and other structural characteristics such as the Si-Si pair distribution functions and the Si-O-Si bond angle distribution, which are compared to the experimental results obtained by direct imaging.
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