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Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I{it h} at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.
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We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the SCAN meta-GGA functional approximation, and carry out systematic comparisons with the results obtained from the GGA-level PBE functional, and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.
The nature of the CH2Cl2 neutral/acidic hydrolysis reaction from ambient to supercritical conditions (25 C to 600 C at 246 bar) is explored. Of primary interest is the effect of the changing dielectric behavior of the water solvent over this temperature range on this reaction. Experiments reveal that significant CH2Cl2 hydrolysis occurs under subcritical temperatures, while relatively little hydrolysis occurs under supercritical conditions. These trends cannot be explain by simple Arrhenius behavior. A combination of Kirkwood theory and ab initio modeling provides a means of successfully accounting for this behavior both qualitatively and quantitatively. The results show that increases in the activation energy and a changing reaction profile with a decreasing dielectric constant provide a mechanism for a slowing of the reaction at higher temperatures by as much as three orders of magnitude. These solvent effects are captured quantitatively in a correction factor to the Arrenius form of the rate constant, which is incorporated into a global rate expression proposed for CH2Cl2 hydrolysis that provides good predictions of the experimental data.
This lecture note reviews recently proposed sparse-modeling approaches for efficient ab initio many-body calculations based on the data compression of Greens functions. The sparse-modeling techniques are based on a compact orthogonal basis representation, intermediate representation (IR) basis functions, for imaginary-time and Matsubara Greens functions. A sparse sampling method based on the IR basis enables solving diagrammatic equations efficiently. We describe the basic properties of the IR basis, the sparse sampling method and its applications to ab initio calculations based on the GW approximation and the Migdal-Eliashberg theory. We also describe a numerical library for the IR basis and the sparse sampling method, irbasis, and provide its sample codes. This lecture note follows the Japanese review article [H. Shinaoka et al., Solid State Physics 56(6), 301 (2021)].
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each phase.
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