Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.

Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. This is particularly true for interactions mediated by short linear motifs occurring in disordered regions of proteins. We find that AlphaFold-Multimer predicts with high sensitivity but limited specificity structures of domain-motif interactions when using small protein fragments as input. Sensitivity decreased substantially when using long protein fragments or full length proteins. We delineated a protein fragmentation strategy particularly suited for the prediction of domain-motif interfaces and applied it to interactions between human proteins associated with neurodevelopmental disorders. This enabled the prediction of highly confident and likely disease-related novel interfaces, which we further experimentally corroborated for FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

Machine Learning for Polaritonic Chemistry: Accessing Chemical Kinetics.

Altering chemical reactivity and material structure in confined optical environments is on the rise, and yet, a conclusive understanding of the microscopic mechanisms remains elusive. This originates mostly from the fact that accurately predicting vibrational and reactive dynamics for soluted ensembles of realistic molecules is no small endeavor, and adding (collective) strong light-matter interaction does not simplify matters. Here, we establish a framework based on a combination of machine learning (ML) models, trained using density-functional theory calculations and molecular dynamics to accelerate such simulations. We then apply this approach to evaluate strong coupling, changes in reaction rate constant, and their influence on enthalpy and entropy for the deprotection reaction of 1-phenyl-2-trimethylsilylacetylene, which has been studied previously both experimentally and using ab initio simulations. While we find qualitative agreement with critical experimental observations, especially with regard to the changes in kinetics, we also find differences in comparison with previous theoretical predictions. The features for which the ML-accelerated and ab initio simulations agree show the experimentally estimated kinetic behavior. Conflicting features indicate that a contribution of dynamic electronic polarization to the reaction process is more relevant than currently believed. Our work demonstrates the practical use of ML for polaritonic chemistry, discusses limitations of common approximations, and paves the way for a more holistic description of polaritonic chemistry.

Comparison of post-COVID-19 symptoms in patients infected with the SARS-CoV-2 variants delta and omicron-results of the Cross-Sectoral Platform of the German National Pandemic Cohort Network (NAPKON-SUEP).

PURPOSE: The influence of new SARS-CoV-2 variants on the post-COVID-19 condition (PCC) remains unanswered. Therefore, we examined the prevalence and predictors of PCC-related symptoms in patients infected with the SARS-CoV-2 variants delta or omicron. METHODS: We compared prevalences and risk factors of acute and PCC-related symptoms three months after primary infection (3MFU) between delta- and omicron-infected patients from the Cross-Sectoral Platform of the German National Pandemic Cohort Network. Health-related quality of life (HrQoL) was determined by the EQ-5D-5L index score and trend groups were calculated to describe changes of HrQoL between different time points. RESULTS: We considered 758 patients for our analysis (delta: n = 341; omicron: n = 417). Compared with omicron patients, delta patients had a similar prevalence of PCC at the 3MFU (p = 0.354), whereby fatigue occurred most frequently (n = 256, 34%). HrQoL was comparable between the groups with the lowest EQ-5D-5L index score (0.75, 95% CI 0.73-0.78) at disease onset. While most patients (69%, n = 348) never showed a declined HrQoL, it deteriorated substantially in 37 patients (7%) from the acute phase to the 3MFU of which 27 were infected with omicron. CONCLUSION: With quality-controlled data from a multicenter cohort, we showed that PCC is an equally common challenge for patients infected with the SARS-CoV-2 variants delta and omicron at least for the German population. Developing the EQ-5D-5L index score trend groups showed that over two thirds of patients did not experience any restrictions in their HrQoL due to or after the SARS-CoV-2 infection at the 3MFU. CLINICAL TRAIL REGISTRATION: The cohort is registered at ClinicalTrials.gov since February 24, 2021 (Identifier: NCT04768998).

Estimates of protection levels against SARS-CoV-2 infection and severe COVID-19 in Germany before the 2022/2023 winter season: the IMMUNEBRIDGE project.

PURPOSE: Despite the need to generate valid and reliable estimates of protection levels against SARS-CoV-2 infection and severe course of COVID-19 for the German population in summer 2022, there was a lack of systematically collected population-based data allowing for the assessment of the protection level in real time. METHODS: In the IMMUNEBRIDGE project, we harmonised data and biosamples for nine population-/hospital-based studies (total number of participants n = 33,637) to provide estimates for protection levels against SARS-CoV-2 infection and severe COVID-19 between June and November 2022. Based on evidence synthesis, we formed a combined endpoint of protection levels based on the number of self-reported infections/vaccinations in combination with nucleocapsid/spike antibody responses ("confirmed exposures"). Four confirmed exposures represented the highest protection level, and no exposure represented the lowest. RESULTS: Most participants were seropositive against the spike antigen; 37% of the participants ≥ 79 years had less than four confirmed exposures (highest level of protection) and 5% less than three. In the subgroup of participants with comorbidities, 46-56% had less than four confirmed exposures. We found major heterogeneity across federal states, with 4-28% of participants having less than three confirmed exposures. CONCLUSION: Using serological analyses, literature synthesis and infection dynamics during the survey period, we observed moderate to high levels of protection against severe COVID-19, whereas the protection against SARS-CoV-2 infection was low across all age groups. We found relevant protection gaps in the oldest age group and amongst individuals with comorbidities, indicating a need for additional protective measures in these groups.

GPAW: An open Python package for electronic structure calculations.

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

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.

The ferroelectric photo ground state of SrTiO3: Cavity materials engineering.

Optical cavities confine light on a small region in space, which can result in a strong coupling of light with materials inside the cavity. This gives rise to new states where quantum fluctuations of light and matter can alter the properties of the material altogether. Here we demonstrate, based on first-principles calculations, that such light-matter coupling induces a change of the collective phase from quantum paraelectric to ferroelectric in the [Formula: see text] ground state, which has thus far only been achieved in out-of-equilibrium strongly excited conditions [X. Li et al., Science 364, 1079-1082 (2019) and T. F. Nova, A. S. Disa, M. Fechner, A. Cavalleri, Science 364, 1075-1079 (2019)]. This is a light-matter hybrid ground state which can only exist because of the coupling to the vacuum fluctuations of light, a photo ground state The phase transition is accompanied by changes in the crystal structure, showing that fundamental ground state properties of materials can be controlled via strong light-matter coupling. Such a control of quantum states enables the tailoring of materials properties or even the design of novel materials purely by exposing them to confined light.

Over 100 years of vitamin E: An overview from synthesis and formulation to application in animal nutrition.

The groundbreaking discovery of vitamin E by Evans and Bishop in 1922 was an important milestone in vitamin research, inspiring further investigation into its crucial role in both human and animal nutrition. Supplementing vitamin E has been proved to enhance multiple key physiological systems such as the reproductive, circulatory, nervous and muscular systems. As the main antioxidant in the blood and on a cellular level, vitamin E maintains the integrity of both cellular and vascular membranes and thus modulates the immune system. This overview showcases important and innovative routes for synthesizing vitamin E on a commercial scale, provides cutting-edge insights into formulation concepts for successful product form development and emphasizes the importance and future of vitamin E in healthy and sustainable animal nutrition.

Shortcut to Self-Consistent Light-Matter Interaction and Realistic Spectra from First Principles.

We introduce a simple approach to how an electromagnetic environment can be efficiently embedded into state-of-the-art electronic structure methods, taking the form of radiation-reaction forces. We demonstrate that this self-consistently provides access to radiative emission, natural linewidth, Lamb shifts, strong coupling, electromagnetically induced transparency, Purcell-enhanced and superradiant emission. As an example, we illustrate its seamless integration into time-dependent density-functional theory with virtually no additional cost, presenting a convenient shortcut to light-matter interactions.

Simulating Terahertz Field-Induced Ferroelectricity in Quantum Paraelectric SrTiO_{3}.

Recent experiments have demonstrated that light can induce a transition from the quantum paraelectric to the ferroelectric phase of SrTiO_{3}. Here, we investigate this terahertz field-induced ferroelectric phase transition by solving the time-dependent lattice Schrödinger equation based on first-principles calculations. We find that ferroelectricity originates from a light-induced mixing between ground and first excited lattice states in the quantum paraelectric phase. In agreement with the experimental findings, our study shows that the nonoscillatory second harmonic generation signal can be evidence of ferroelectricity in SrTiO_{3}. We reveal the microscopic details of this exotic phase transition and highlight that this phenomenon is a unique behavior of the quantum paraelectric phase.

The German National Pandemic Cohort Network (NAPKON): rationale, study design and baseline characteristics.

The German government initiated the Network University Medicine (NUM) in early 2020 to improve national research activities on the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. To this end, 36 German Academic Medical Centers started to collaborate on 13 projects, with the largest being the National Pandemic Cohort Network (NAPKON). The NAPKON's goal is creating the most comprehensive Coronavirus Disease 2019 (COVID-19) cohort in Germany. Within NAPKON, adult and pediatric patients are observed in three complementary cohort platforms (Cross-Sectoral, High-Resolution and Population-Based) from the initial infection until up to three years of follow-up. Study procedures comprise comprehensive clinical and imaging diagnostics, quality-of-life assessment, patient-reported outcomes and biosampling. The three cohort platforms build on four infrastructure core units (Interaction, Biosampling, Epidemiology, and Integration) and collaborations with NUM projects. Key components of the data capture, regulatory, and data privacy are based on the German Centre for Cardiovascular Research. By April 01, 2022, 34 university and 40 non-university hospitals have enrolled 5298 patients with local data quality reviews performed on 4727 (89%). 47% were female, the median age was 52 (IQR 36-62-) and 50 pediatric cases were included. 44% of patients were hospitalized, 15% admitted to an intensive care unit, and 12% of patients deceased while enrolled. 8845 visits with biosampling in 4349 patients were conducted by April 03, 2022. In this overview article, we summarize NAPKON's design, relevant milestones including first study population characteristics, and outline the potential of NAPKON for German and international research activities.Trial registration https://clinicaltrials.gov/ct2/show/NCT04768998 . https://clinicaltrials.gov/ct2/show/NCT04747366 . https://clinicaltrials.gov/ct2/show/NCT04679584.

A perspective on ab initio modeling of polaritonic chemistry: The role of non-equilibrium effects and quantum collectivity.

This Perspective provides a brief introduction into the theoretical complexity of polaritonic chemistry, which emerges from the hybrid nature of strongly coupled light-matter states. To tackle this complexity, the importance of ab initio methods is highlighted. Based on those, novel ideas and research avenues are developed with respect to quantum collectivity, as well as for resonance phenomena immanent in reaction rates under vibrational strong coupling. Indeed, fundamental theoretical questions arise about the mesoscopic scale of quantum-collectively coupled molecules when considering the depolarization shift in the interpretation of experimental data. Furthermore, to rationalize recent findings based on quantum electrodynamical density-functional theory (QEDFT), a simple, but computationally efficient, Langevin framework is proposed based on well-established methods from molecular dynamics. It suggests the emergence of cavity-induced non-equilibrium nuclear dynamics, where thermal (stochastic) resonance phenomena could emerge in the absence of external periodic driving. Overall, we believe that the latest ab initio results indeed suggest a paradigmatic shift for ground-state chemical reactions under vibrational strong coupling from the collective quantum interpretation toward a more local, (semi)-classically and non-equilibrium dominated perspective. Finally, various extensions toward a refined description of cavity-modified chemistry are introduced in the context of QEDFT, and future directions of the field are sketched.

Modification of excitation and charge transfer in cavity quantum-electrodynamical chemistry.

Energy transfer in terms of excitation or charge is one of the most basic processes in nature, and understanding and controlling them is one of the major challenges of modern quantum chemistry. In this work, we highlight that these processes as well as other chemical properties can be drastically altered by modifying the vacuum fluctuations of the electromagnetic field in a cavity. By using a real-space formulation from first principles that keeps all of the electronic degrees of freedom in the model explicit and simulates changes in the environment by an effective photon mode, we can easily connect to well-known quantum-chemical results such as Dexter charge-transfer and Förster excitation-transfer reactions, taking into account the often-disregarded Coulomb and self-polarization interaction. We find that the photonic degrees of freedom introduce extra electron-electron correlations over large distances and that the coupling to the cavity can drastically alter the characteristic charge-transfer behavior and even selectively improve the efficiency. For excitation transfer, we find that the cavity renders the transfer more efficient, essentially distance-independent, and further different configurations of highest efficiency depending on the coherence times. For strong decoherence (short coherence times), the cavity frequency should be in between the isolated excitations of the donor and acceptor, while for weak decoherence (long coherence times), the cavity should enhance a mode that is close to resonance with either donor or acceptor. Our results highlight that changing the photonic environment can redefine chemical processes, rendering polaritonic chemistry a promising approach toward the control of chemical reactions.

Intermolecular interactions in optical cavities: An ab initio QED study.

Intermolecular bonds are weak compared to covalent bonds, but they are strong enough to influence the properties of large molecular systems. In this work, we investigate how strong light-matter coupling inside an optical cavity can modify intermolecular forces and illustrate the varying necessity of correlation in their description. The electromagnetic field inside the cavity can modulate the ground state properties of weakly bound complexes. Tuning the field polarization and cavity frequency, the interactions can be stabilized or destabilized, and electron densities, dipole moments, and polarizabilities can be altered. We demonstrate that electron-photon correlation is fundamental to describe intermolecular interactions in strong light-matter coupling. This work proposes optical cavities as a novel tool to manipulate and control ground state properties, solvent effects, and intermolecular interactions for molecules and materials.

Remote electrochemical modulation of pKa in a rotaxane by co-conformational allostery.

Allosteric control, one of Nature's most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pKa of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pKa to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron- and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.

From Sugar to Nutritional Products - Product Form Development.

The formulation of active ingredients into emulsion- and suspension-based delivery systems offers a wide range of opportunities to produce stable and highly bioavailable product forms for their later application in human and animal nutrition. Recent trends in product form development have focused on using renewable and naturally-derived raw materials to meet the increasing consumer demand on sustainable value chains and nutritional products with 'clean labelling'. Therefore, we reviewed chemical fundamentals and application examples of plant-derived protective hydrocolloids with highly potent emulsifying capacity, in particular, modified starches, pectin, and lignosulfonates, for the formulation of vitamins, carotenoids, and other active ingredients.

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).

[Medical device training in arthroplasty : National practice and quality standards]. / Medizinprodukteschulungen in der Endoprothetik : Nationale Praxis und Qualitätsansprüche.

The qualified training of users of medicinal products is enshrined in law by the Medical Devices Act. In this article, a survey and analysis of the training measures for arthroplasty of the large joints offered by distributors of medical devices is carried out. To that end, the internet presence of suppliers of medical devices was evaluated with regard to the training measures on offer, and selected suppliers were sent questionnaires. The presentation of the available training programmes on the websites was incomplete. Even after the amendment of the Medical Devices Act, this has only slightly changed; however, legally required instructions for use were available for all distributors questioned. In some cases, there are large gaps in the range of modern training methods on offer, such as practical instruction, multimedia offerings or visual-haptic training methods.

Relative spectral tuning of the vertical versus base modes in plasmonic nanocones.

Gold nanocones acting as optical antennas offer an excellent geometry for focusing light near the cone tip, acting as nano-light sources with spot sizes on the order of the tip radius. However only the vertical plasmon mode oscillating in the axial direction can effectively excite the tip, whereas lateral modes oscillating along the cone base create mostly unwanted background in applications. The present work investigates the three-dimensional plasmonic mode structure of nanocones both experimentally and numerically. By tuning the nanocone aspect ratio, the modes can be spectrally tuned relative to each other, making them coincide for maximum excitation, or tuning the base mode away from the vertical mode for effective background suppression.

Benchmarking semiclassical and perturbative methods for real-time simulations of cavity-bound emission and interference.

We benchmark a selection of semiclassical and perturbative dynamics techniques by investigating the correlated evolution of a cavity-bound atomic system to assess their applicability to study problems involving strong light-matter interactions in quantum cavities. The model system of interest features spontaneous emission, interference, and strong coupling behavior and necessitates the consideration of vacuum fluctuations and correlated light-matter dynamics. We compare a selection of approximate dynamics approaches including fewest switches surface hopping (FSSH), multitrajectory Ehrenfest dynamics, linearized semiclassical dynamics, and partially linearized semiclassical dynamics. Furthermore, investigating self-consistent perturbative methods, we apply the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy in the second Born approximation. With the exception of fewest switches surface hopping, all methods provide a reasonable level of accuracy for the correlated light-matter dynamics, with most methods lacking the capacity to fully capture interference effects.