Making ab initio QED functional(s): Nonperturbative and photon-free effective frameworks for strong light-matter coupling.

Strong light-matter coupling provides a promising path for the control of quantum matter where the latter is routinely described from first principles. However, combining the quantized nature of light with this ab initio tool set is challenging and merely developing as the coupled light-matter Hilbert space is conceptually different and computational cost quickly becomes overwhelming. In this work, we provide a nonperturbative photon-free formulation of quantum electrodynamics (QED) in the long-wavelength limit, which is formulated solely on the matter Hilbert space and can serve as an accurate starting point for such ab initio methods. The present formulation is an extension of quantum mechanics that recovers the exact results of QED for the zero- and infinite-coupling limit and the infinite-frequency as well as the homogeneous limit, and we can constructively increase its accuracy. We show how this formulation can be used to devise approximations for quantum-electrodynamical density-functional theory (QEDFT), which in turn also allows us to extend the ansatz to the full minimal-coupling problem and to nonadiabatic situations. Finally, we provide a simple local density-type functional that takes the strong coupling to the transverse photon degrees of freedom into account and includes the correct frequency and polarization dependence. This QEDFT functional accounts for the quantized nature of light while remaining computationally simple enough to allow its application to a large range of systems. All approximations allow the seamless application to periodic systems.

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel.

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity. IMPORTANCE: New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa.

BACKGROUND: Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes. METHODS: In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and "masked" (RGP-free) genomes, and to what extent this variation differs among the phylogroups. FINDINGS: We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses. INTERPRETATION: Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes. FUNDING: German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.

Light-Matter Hybrid-Orbital-Based First-Principles Methods: The Influence of Polariton Statistics.

A detailed understanding of strong matter-photon interactions requires first-principle methods that can solve the fundamental Pauli-Fierz Hamiltonian of nonrelativistic quantum electrodynamics efficiently. A possible way to extend well-established electronic-structure methods to this situation is to embed the Pauli-Fierz Hamiltonian in a higher-dimensional light-matter hybrid auxiliary configuration space. In this work we show the importance of the resulting hybrid Fermi-Bose statistics of the polaritons, which are the new fundamental particles of the "photon-dressed" Pauli-Fierz Hamiltonian for systems in cavities. We show that violations of these statistics can lead to unphysical results. We present an efficient way to ensure the correct statistics by enforcing representability conditions on the dressed one-body reduced density matrix. We further present a general prescription how to extend a given first-principles approach to polaritons and as an example introduce polaritonic Hartree-Fock theory. While being a single-reference method in polariton space, polaritonic Hartree-Fock is a multireference method in the electronic space, i.e., it describes electronic correlations. We also discuss possible applications to polaritonic QEDFT. We apply this theory to a lattice model and find that, the more delocalized the bound-state wave function of the particles is, the stronger it reacts to photons. The main reason is that within a small energy range, many states with different electronic configurations are available as opposed to a strongly bound (and hence energetically separated) ground-state wave function. This indicates that under certain conditions coupling to the quantum vacuum of a cavity can indeed modify ground state properties.

Ruthenium phthalocyanine-bipyridyl dyads as sensitizers for dye-sensitized solar cells: dye coverage versus molecular efficiency.

The application of ruthenium phthalocyanine complexes as sensitizing dyes in dye-sensitized solar cells (DSCs) is explored. Four monomeric complexes are reported which vary in peripheral substitution and axial ligand anchoring groups. Sensitizing dyes containing two ruthenium centers are also presented. These dyads, which contain ruthenium phthalocyanine and bipyridyl chromophores, were prepared using a protection/deprotection strategy that allows for convenient purification. DSCs fabricated using the phthalocyanine complexes and dyads were less efficient than those incorporating a standard DSC dye. However, on the basis of the number of molecules bound to the TiO(2) electrode surfaces, several of the new complexes were more efficient at photocurrent generation. The results highlight the importance of molecular size, and thus the dye coverage of the electrode surface in the design of new sensitizing dyes.

Reduced Density-Matrix Approach to Strong Matter-Photon Interaction.

We present a first-principles approach to electronic many-body systems strongly coupled to cavity modes in terms of matter-photon one-body reduced density matrices. The theory is fundamentally nonperturbative and thus captures not only the effects of correlated electronic systems but accounts also for strong interactions between matter and photon degrees of freedom. We do so by introducing a higher-dimensional auxiliary system that maps the coupled fermion-boson system to a dressed fermionic problem. This reformulation allows us to overcome many fundamental challenges of density-matrix theory in the context of coupled fermion-boson systems and we can employ conventional reduced density-matrix functional theory developed for purely fermionic systems. We provide results for one-dimensional model systems in real space and show that simple density-matrix approximations are accurate from the weak to the deep-strong coupling regime. This justifies the application of our method to systems that are too complex for exact calculations and we present first results, which show that the influence of the photon field depends sensitively on the details of the electronic structure.

Kinetic-Energy Density-Functional Theory on a Lattice.

We present a kinetic-energy density-functional theory and the corresponding kinetic-energy Kohn-Sham (keKS) scheme on a lattice and show that, by including more observables explicitly in a density-functional approach, already simple approximation strategies lead to very accurate results. Here, we promote the kinetic-energy density to a fundamental variable alongside the density and show for specific cases (analytically and numerically) that there is a one-to-one correspondence between the external pair of on-site potential and site-dependent hopping and the internal pair of density and kinetic-energy density. On the basis of this mapping, we establish two unknown effective fields, the mean-field exchange-correlation potential and the mean-field exchange-correlation hopping, which force the keKS system to generate the same kinetic-energy density and density as the fully interacting one. We show, by a decomposition based on the equations of motions for the density and the kinetic-energy density, that we can construct simple orbital-dependent functionals that outperform the corresponding exact-exchange Kohn-Sham (KS) approximation of standard density-functional theory. We do so by considering the exact KS and keKS systems and comparing the unknown correlation contributions as well as by comparing self-consistent calculations based on the mean-field exchange (for the effective potential) and a uniform (for the effective hopping) approximation for the keKS and the exact-exchange approximation for the KS system, respectively.