Validation of a computational model for a coupled liquid and gas flow in micro-nozzles

The work presents verification of a numerical model for micro-jet focusing, where a coupled liquid and gas flow occurs in a gas dynamic virtual nozzle (GDVN). Nozzles of this type are used in serial femtosecond crystallography experiments to deliver samples into X-ray beam. The following performance criteria are desirable: the jet to be longer than 100 µm to avoid nozzle shadowing, the diameter as small as possible to minimize the background signal, and the jet velocity as high as possible to avoid sample’s double X-ray exposure. Previous comprehensive numerical investigation has been extended to include numerical analysis of the tip jet velocities. These simulations were then compared with the experimental data. The coupled numerical model of a 3D printed GDVN considers a laminar two-phase, Newtonian, compressible flow, which is solved based on the finite volume method discretization and interface tracking with volume of fluid (VOF). The numerical solution is calculated with OpenFOAM based compressible interFoam solver, which uses algebraic formulation of VOF. In experimental setup for model validation a 3D printed GDVN was inserted in a vacuum chamber with two windows used for illumination and visualization. Once the jet was stabilized its velocity was estimated based on a distance a droplet traveled between two consecutive illumination pulses with a known time delay. The experimental and computational study was performed for a constant liquid flow rate of 14 l/min and the gas mass flow rate in the range from 5 mg/min to 25 mg/min. The coupled numerical model reasonably predicts the jet speed and shape as a function of the gas flow

Subsurface Flows in and Around Active Regions with Rotating and Non-rotating Sunspots

The temporal variation of the horizontal velocity in subsurface layers beneath three different types of active regions is studied using the technique of ring diagrams. In this study, we select active regions (ARs) 10923, 10930, 10935 from three consecutive Carrington rotations: AR 10930 contains a fast-rotating sunspot in a strong emerging active region while other two have non-rotating sunspots with emerging flux in AR 10923 and decaying flux in AR 10935. The depth range covered is from the surface to about 12 Mm. In order to minimize the influence of systematic effects, the selection of active and quiet regions is made so that these were observed at the same heliographic locations on the solar disk. We find a significant variation in both components of the horizontal velocity in active regions as compared to quiet regions. The magnitude is higher in emerging-flux regions than in the decaying-flux region, in agreement with earlier findings. Further, we clearly see a significant temporal variation in depth profiles of both zonal and meridional flow components in AR 10930, with the variation in the zonal component being more pronounced. We also notice a significant influence of the plasma motion in areas closest to the rotating sunspot in AR 10930 while areas surrounding the non-rotating sunspots in all three cases are least affected by the presence of the active region in their neighborhood.Comment: Solar Physics (in press), includes 11 figure

Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease

Here we present the crystal structure of SARS-CoV-2 main protease (Mpro) covalently bound to 2-methyl-1-tetralone. This complex was obtained by co-crystallization of Mpro with HEAT (2-(((4-hydroxyphenethyl)amino)methyl)-3,4-dihydronaphthalen-1(2H)-one) in the framework of a large X-ray crystallographic screening project of Mpro against a drug repurposing library, consisting of 5632 approved drugs or compounds in clinical phase trials. Further investigations showed that HEAT is cleaved by Mpro in an E1cB-like reaction mechanism into 2-methylene-1-tetralone and tyramine. The catalytic Cys145 subsequently binds covalently in a Michael addition to the methylene carbon atom of 2-methylene-1-tetralone. According to this postulated model HEAT is acting in a pro-drug-like fashion. It is metabolized by Mpro, followed by covalent binding of one metabolite to the active site. The structure of the covalent adduct elucidated in this study opens up a new path for developing non-peptidic inhibitors

Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals

High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract No. DE-AC02-76SF00515. Parts of the sample delivery system used at LCLS for this research were funded by the NIH grant P41GM103393, formerly P41RR001209. In addition to DESY, this work has been supported by the excellence cluster ‘The Hamburg Center for Ultrafast Imaging – Structure, Dynamics and Control of Matter at the Atomic Scale’ of the Deutsche Forschungsgemeinschaft (CUI, DFG-EXC1074), the Gottfried Wilhelm Leibniz Program of the DFG, the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013) through the Synergy Grant AXSIS (ERC-2013-SyG 609920) and the Consolidator Grant COMOTION (ERC-Ku¨pper-614507), the Helmholtz Association ‘Initiative and Networking Fund’, and the Australian Research Council’s Discovery Projects funding scheme (DP170100131). RAK acknowledges support from an NSF STC award (1231306)

Massive X-ray screening reveals two allosteric drug binding sites of SARS-CoV-2 main protease

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous health problems and economical challenges for mankind. To date, no effective drug is available to directly treat the disease and prevent virus spreading. In a search for a drug against COVID-19, we have performed a massive X-ray crystallographic screen of repurposing drug libraries containing 5953 individual compounds against the SARS-CoV-2 main protease (Mpro), which is a potent drug target as it is essential for the virus replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds binding to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and five non-peptidic compounds showed antiviral activity at non-toxic concentrations. Interestingly, two compounds bind outside the active site to the native dimer interface in close proximity to the S1 binding pocket. Another compound binds in a cleft between the catalytic and dimerization domain of Mpro. Neither binding site is related to the enzymatic active site and both represent attractive targets for drug development against SARS-CoV-2. This X-ray screening approach thus has the potential to help deliver an approved drug on an accelerated time-scale for this and future pandemics

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M^(pro)), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M^(pro). In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2

X ray screening identifies active site and allosteric inhibitors of SARS CoV 2 main protease

The coronavirus disease COVID 19 caused by SARS CoV 2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID 19, we have performed a high throughput x ray crystallographic screen of two repurposing drug libraries against the SARS CoV 2 main protease Mpro , which is essential for viral replication. In contrast to commonly applied x ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS CoV

Validation of a computational model for a coupled liquid and gas flow in micro-nozzles

The work presents verification of a numerical model for micro-jet focusing, where a coupled liquid and gas flow occurs in a gas dynamic virtual nozzle (GDVN). Nozzles of this type are used in serial femtosecond crystallography experiments to deliver samples into X-ray beam. The following performance criteria are desirable: the jet to be longer than 100 µm to avoid nozzle shadowing, the diameter as small as possible to minimize the background signal, and the jet velocity as high as possible to avoid sample’s double X-ray exposure. Previous comprehensive numerical investigation has been extended to include numerical analysis of the tip jet velocities. These simulations were then compared with the experimental data. The coupled numerical model of a 3D printed GDVN considers a laminar two-phase, Newtonian, compressible flow, which is solved based on the finite volume method discretization and interface tracking with volume of fluid (VOF). The numerical solution is calculated with OpenFOAM based compressible interFoam solver, which uses algebraic formulation of VOF. In experimental setup for model validation a 3D printed GDVN was inserted in a vacuum chamber with two windows used for illumination and visualization. Once the jet was stabilized its velocity was estimated based on a distance a droplet traveled between two consecutive illumination pulses with a known time delay. The experimental and computational study was performed for a constant liquid flow rate of 14 l/min and the gas mass flow rate in the range from 5 mg/min to 25 mg/min. The coupled numerical model reasonably predicts the jet speed and shape as a function of the gas flow

Validation of a Computational Model for a Coupled Liquid and Gas Flow in Micro-Nozzles

The work presents verification of a numerical model for micro-jet focusing, where a coupled liquid and gas flow occurs in a gas dynamic virtual nozzle (GDVN). Nozzlesof this type are usedinserial femtosecond crystallographyexperimentsto deliver samplesintoX-ray beam. Thefollowing performance criteria are desirable: the jet to be longer than 100 μm to avoid nozzle shadowing, the diameter as small as possibleto minimize the background signal,and the jet velocityas high as possible to avoid sample’sdouble X-ray exposure.Previouscomprehensive numerical investigation has been extended to includenumerical analysis of the tip jet velocities. These simulations were then comparedwith the experimental data. The coupled numerical model of a 3D printed GDVN considers a laminar two-phase, Newtonian, compressible flow, which is solved based on the finite volume method discretization and interface tracking with volume of fluid (VOF). The numerical solution is calculated with OpenFOAM based compressible interFoam solver, which uses algebraicformulation of VOF. In experimental setupfor model validationa 3D printed GDVN was inserted in a vacuum chamber with two windows used for illumination and visualization. Once the jet was stabilized its velocity wasestimated based on a distance a droplet traveled between two consecutive illumination pulseswith a known time delay. The experimental and computational study was performed for a constant liquid flow rate of 14 $\mu$l/min and the gas mass flow rate in the range from 5 mg/min to 25 mg/min. The coupled numerical model reasonablypredictsthe jet speed and shape as a function of the gas flow

The natural breakup length of a steady capillary jet

72 American Physical Society Division of Fluid Dynamics 2019Despite their fundamental and applied importance, a general model to predict the natural breakup length of steady capillary jets has not been proposed yet. In this work, we derive a scaling law with two universal constants to calculate that length as a function of the liquid properties and operating conditions. These constants are determined by fitting the scaling law to a large set of experimental and numerical measurements, including previously published data. Both the experimental and numerical jet lengths conform remarkably well to the proposed scaling law. This law is explained in terms of the growth of perturbations excited by the jet breakup itself