Comparison of macro- and microscopic solutions of the Riemann problem I. Supercritical shock tube and expansion into vacuum

The Riemann problem is a fundamental concept in the development of numerical methods for the macroscopic flow equations. It allows the resolution of discontinuities in the solution, such as shock waves, and provides a powerful tool for the construction of numerical flux functions. A natural extension of the Riemann problem involves two phases, a liquid and a vapour phase which undergo phase change at the material boundary. For this problem, we aim at a comparison with the macroscopic solution from molecular dynamics simulations. In this work, as a first step, the macroscopic solution of two important Riemann problem scenarios, the supercritical shock tube and the expansion into vacuum, were compared to microscopic solutions produced by molecular dynamics simulations. High fidelity equations of state were used to accurately approximate the material behaviour of the model fluid. The results of both scenarios compare almost perfect with each other. During the vacuum expansion, the fluid obtained a state of non-equilibrium, where the microscopic and macroscopic solutions start to diverge. A limiting case was shown, where liquid droplets appeared in the expansion fan, which was approximated by the macroscopic solution, assuming an undercooled vapour.DFG, 84292822, TRR 75: Tropfendynamische Prozesse unter extremen Umgebungsbedingunge

Glass transition of charged particles in two-dimensional confinement

The glass transition of mesoscopic charged particles in two-dimensional confinement is studied by mode-coupling theory. We consider two types of effective interactions between the particles, corresponding to two different models for the distribution of surrounding ions that are integrated out in coarse-grained descriptions. In the first model, a planar monolayer of charged particles is immersed in an unbounded isotropic bath of ions, giving rise to an isotropically screened Debye-H\"uckel- (Yukawa-) type effective interaction. The second, experimentally more relevant system is a monolayer of negatively charged particles that levitate atop a flat horizontal electrode, as frequently encountered in laboratory experiments with complex (dusty) plasmas. A steady plasma current towards the electrode gives rise to an anisotropic effective interaction potential between the particles, with an algebraically long-ranged in-plane decay. In a comprehensive parameter scan that covers the typical range of experimentally accessible plasma conditions, we calculate and compare the mode-coupling predictions for the glass transition in both kinds of systems.Comment: 10 pages, 8 figure

Diffusion limited evaporation of a binary liquid film

An analytical solution of a model fluid’s time behavior, known as the Stefan problem, is presented. A scenario is investigated in which a planar two-component liquid film is continuously evaporating into a thermodynamically non-ideal vapor phase. Evaporation is initiated and maintained by a spatial chemical potential gradient, while its rate is limited by the components’ diffusion fluxes across the vapor-liquid interface. Local thermodynamic equilibrium is found to be present throughout the process. In contrast to the classical approach relying on equations of state, all required non-idealities are formulated in relation to the Gibbs energy and are determined by molecular simulations. Initially, the liquid is an equimolar mixture of two components of different volatility, whereas the adjacent vapor phase is dominated by a dense inert gas. To validate the analytical model and verify all exploited assumptions, the results are contrasted to large scale molecular dynamics simulations

KATP Channel Openers Have Opposite Effects on Mitochondrial Respiration Under Different Energetic Conditions

Mitochondrial (m) KATP channel opening has been implicated in triggering cardiac preconditioning. Its consequence on mitochondrial respiration, however, remains unclear. We investigated the effects of two different KATP channel openers and antagonists on mitochondrial respiration under two different energetic conditions. Oxygen consumption was measured for complex I (pyruvate/malate) or complex II (succinate with rotenone) substrates in mitochondria from fresh guinea pig hearts. One of two mKATP channel openers, pinacidil or diazoxide, was given before adenosine diphosphate in the absence or presence of an mKATP channel antagonist, glibenclamide or 5-hydroxydecanoate. Without ATP synthase inhibition, both mKATP channel openers differentially attenuated mitochondrial respiration. Neither mKATP channel antagonist abolished these effects. When ATP synthase was inhibited by oligomycin to decrease [ATP], both mKATP channel openers accelerated respiration for both substrate groups. This was abolished by mKATP channel blockade. Thus, under energetically more physiological conditions, the main effect of mKATP channel openers on mitochondrial respiration is differential inhibition independent of mKATP channel opening. In contrast, under energetically less physiological conditions, mKATP channel opening can be evidenced by accelerated respiration and blockade by antagonists. Therefore, the effects of mKATP channel openers on mitochondrial function likely depend on the experimental conditions and the cell\u27s underlying energetic state

Evaporation sampled by stationary molecular dynamics simulation

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 151, 044704 (2019) and may be found at https://doi.org/10.1063/1.5111759.A nonequilibrium method is developed to sample evaporation of a liquid across a planar interface in a stationary scenario by molecular dynamics. The method does not rely on particle insertions which are challenging when they are used to maintain mass conservation. Its algorithm has a low complexity and is well suited for massively parallel simulations that may yield results with an excellent statistical accuracy. Spatially resolved classical profiles, e.g., for temperature, density, and force, are sampled with a high resolution for a varying hydrodynamic velocity of the evaporation flow. Relatively large systems are simulated, allowing for a detailed study of velocity distribution functions. Varying the hydrodynamic velocity from zero to the speed of sound, it is found that the evaporation flux increases asymptotically, reaching about 90% of its maximum value when the hydrodynamic velocity is about half of its maximum value. A deviation from the Maxwell distribution is identified for the transversal particle velocity near the interface which selectively hinders the migration of individual particles from liquid to vapor with its potential well, allowing only the faster ones to escape. The vapor region in the vicinity of the interface exhibits a spread between the transversal and longitudinal temperature, but equipartition is reattained through particle interactions such that Maxwell distributions are found at a certain distance from the interface. A detailed discussion of the atomistic mechanisms during evaporation is provided, facilitating understanding of this ubiquitous process.DFG, 84292822, TRR 75: Tropfendynamische Prozesse unter extremen UmgebungsbedingungenDFG, 397387079, Tropfen unter Temperatur- und Geschwindigkeitsgradienten mittels atomistischer Simulation (B06*

Improving the defect tolerance of PBF-LB/M processed 316L steel by increasing the nitrogen content

Nitrogen (N) in steels can improve their mechanical strength by solid solution strengthening. Processing N-alloyed steels with additive manufacturing, here laser powder bed fusion (PBF-LB), is challenging as the N-solubility in the melt can be exceeded. This degassing of N counteracts its intended positive effects. Herein, the PBF-LB processed 316L stainless steel with increased N-content is investigated and compared to PBF-LB 316L with conventional N-content. The N is introduced into the steel by nitriding the powder and mixing it with the starting powder to achieve an N-content of approximately 0.16 mass%. Thermodynamic calculations for maximum solubility to avoid N outgassing and pore formation under PBF-LB conditions are performed beforehand. Based on the results, a higher defect tolerance under fatigue characterized by Murakami model can be achieved without negatively influencing the PBF-LB processability of the 316L steel. The increased N-content leads to higher hardness (+14%), yield strength (+16%), tensile strength (+9%), and higher failure stress in short time fatigue test (+16%)

TweTriS: Twenty trillion-atom simulation

Significant improvements are presented for the molecular dynamics code ls1 mardyn — a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell-based force calculation are presented, which are able to retain Newton’s third law optimization. Comparisons to well-optimized Verlet list-based codes, such as LAMMPS and GROMACS, demonstrate the viability of the linked cell-based approach. The present version of ls1 mardyn is used to run simulations on entire supercomputers, maximizing the number of sampled atoms. Compared to the preceding version of ls1 mardyn on the entire set of 9216 nodes of SuperMUC, Phase 1, 27% more atoms are simulated. Weak scaling performance is increased by up to 40% and strong scaling performance by up to more than 220%. On Hazel Hen, strong scaling efficiency of up to 81% and 189 billion molecule updates per second is attained, when scaling from 8 to 7168 nodes. Moreover, a total of 20 trillion atoms is simulated at up to 88% weak scaling efficiency running at up to 1.33 PFLOPS. This represents a fivefold increase in terms of the number of atoms simulated to date.BMBF, 01IH16008, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der Partikelsimulatio

Inhibitors of dihydroorotate dehydrogenase cooperate with molnupiravir and N4-hydroxycytidine to suppress SARS-CoV-2 replication

Funding Information: We thank Thorsten Wolff, Daniel Bourquain, Jessica Schulz, and Christian Mache from the Robert-Koch Institute and Martin Beer from the Friedrich Loeffler Institute (FLI) for providing isolates of SARS-CoV-2 variants. We thank Anna Kraft and Gabriele Czerwinski (both FLI) for support in the preparation of samples for pathology, and Catherine Hambly (University of Aberdeen) for help with daily energy expenditure measurements. We would like to thank Cathrin Bierwirth (University Medical Center Göttingen), Isabell Schulz, Anne-Kathrin Donner, and Frank-Thorben Peters for excellent technician assistance and Jasmin Fertey and Alexandra Rockstroh for providing the virus stocks for the mice experiment (Fraunhofer Institute IZI Leipzig). We acknowledge support by the Open Access Publication Funds of the Göttingen University. KMS was a member of the Göttingen Graduate School GGNB during this work. This work was funded by the COVID-19 Forschungsnetzwerk Niedersachsen (COFONI) to MD, by the Federal Ministry of Education and Research Germany ( Bundesministerium für Bildung und Forschung; BMBF ; OrganSARS , 01KI2058 ) to SP and TM, and by a grant of the Max Planck Foundation to DG. Declaration of interests AS, HK, EP, and DV are employees of Immunic AG and own shares and/or stock-options of the parent company of Immunic AG, Immunic Inc. Some of the Immunic AG employees also hold patents for the Immunic compounds described in this manuscript (WO2012/001,148, WO03006425). KMS, AD, and MD are employees of University Medical Center Göttingen, which has signed a License Agreement with Immunic AG covering the combination of DHODH inhibitors and nucleoside analogs to treat viral infections, including COVID-19 (inventors: MD, KMS, and AD). The other authors declare no conflict of interest.Peer reviewedPublisher PD

In-depth analysis of T cell immunity and antibody responses in heterologous prime-boost-boost vaccine regimens against SARS-CoV-2 and Omicron variant.

With the emergence of novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Variants of Concern (VOCs), vaccination studies that elucidate the efficiency and effectiveness of a vaccination campaign are critical to assess the durability and the protective immunity provided by vaccines. SARS-CoV-2 vaccines have been found to induce robust humoral and cell-mediated immunity in individuals vaccinated with homologous vaccination regimens. Recent studies also suggest improved immune response against SARS-CoV-2 when heterologous vaccination strategies are employed. Yet, few data exist on the extent to which heterologous prime-boost-boost vaccinations with two different vaccine platforms have an impact on the T cell-mediated immune responses with a special emphasis on the currently dominantly circulating Omicron strain. In this study, we collected serum and peripheral blood mononuclear cells (PBMCs) from 57 study participants of median 35-year old's working in the health care field, who have received different vaccination regimens. Neutralization assays revealed robust but decreased neutralization of Omicron VOC, including BA.1 and BA.4/5, compared to WT SARS-CoV-2 in all vaccine groups and increased WT SARS-CoV-2 binding and neutralizing antibodies titers in homologous mRNA prime-boost-boost study participants. By investigating cytokine production, we found that homologous and heterologous prime-boost-boost-vaccination induces a robust cytokine response of CD4+ and CD8+ T cells. Collectively, our results indicate robust humoral and T cell mediated immunity against Omicron in homologous and heterologous prime-boost-boost vaccinated study participants, which might serve as a guide for policy decisions