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We present measurements of the damping experienced by custom-made quartz tuning forks submerged in 3He covering frequencies from 20 to 600 kHz. Measurements were conducted in the bulk of normal liquid 3He at temperatures from 1.5 K down to 12 mK and in superfluid 3He-B well below the critical temperature. The presented results complement earlier work on tuning fork damping in 3He, removing possible ambiguities associated with acoustic emission within partially enclosed volumes and extend the probed range of frequencies, leading to a clearly established frequency dependence of the acoustic losses. Our results validate existing models of damping and point toward the same mechanism of wave emission of first sound in normal 3He and liquid 4He and zero sound in superfluid 3He. We observe a steep frequency dependence of the damping ≈ f 5.5, which starts to dominate around 100 kHz and restricts the use of tuning forks as efficient sensors in quantum fluids. The acoustic emission model can predict the limiting frequencies for various devices, including micro-electromechanical and nano-electromechanical structures developed for quantum turbulence and single vortex dynamics research.

Summary Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. Availability and Implementation Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. Supplementary information Supplementary data are available at Bioinformatics online.

Superconducting heat switches with extremely low normal state resistances are needed for constructing continuous nuclear demagnetization refrigerators with high cooling power. Aluminum is a suitable superconductor for the heat switch because of its high Debye temperature and its commercial availability in high purity. We have constructed a high quality Al heat switch whose design is significantly different than that of previous heat switches. In order to join the Al to Cu with low contact resistance, we plasma etched the Al to remove its oxide layer and then immediately deposited Au without breaking the vacuum of the e-beam evaporator. In the normal state of the heat switch, we measured a thermal conductance of 8 T W/K2, which is equivalent to an electrical resistance of 3 nΩ according to the Wiedemann–Franz law. In the superconducting state, we measured a thermal conductance that is 2 × 106 times lower than that of the normal state at 50 mK.

We report an experimental study of oscillatory thermal counterflow of superfluid $^{4}\mathrm{He}$ and its transition to quantum turbulence inspired by the work of Kotsubo and Swift [Phys. Rev. Lett. 62, 2604 (1989)]. We use a pair of transversally oriented second-sound sensors to provide direct proof that upon exceeding a critical heat flux, quantized vorticity is generated in the antinodes of the longitudinal resonances of the oscillating counterflow. Building on modern understanding of oscillatory flows of superfluid $^{4}\mathrm{He}$ [D. Schmoranzer et al., Phys. Rev. B 99, 054511 (2019)], we re-evaluate the original data together with ours and provide grounds for the previously unexplained temperature dependence of critical velocities. Our analysis incorporates a classical flow instability in the normal component described by the dimensionless Donnelly number, which is shown to trigger quantum turbulence at temperatures below $\ensuremath{\approx}1.7\phantom{\rule{0.16em}{0ex}}\mathrm{K}$. This contrasts with the original interpretation based on the dynamics of quantized vortices, and we show that for oscillatory counterflow, such an approach is valid only at temperatures above $\ensuremath{\approx}1.8\phantom{\rule{0.16em}{0ex}}\mathrm{K}$. Finally, we demonstrate that the instabilities occurring in oscillatory counterflow are governed by the same underlying physics as those in flow due to submerged oscillators and propose a unified description of high Stokes number coflow and counterflow experiments.

Quantum turbulence—the stochastic motion of quantum fluids such as 4 He and 3 He-B, which display pure superfluidity at zero temperature and two-fluid behavior at finite but low temperatures—has been a subject of intense experimental, theoretical, and numerical studies over the last half a century. Yet, there does not exist a satisfactory phenomenological framework that captures the rich variety of experimental observations, physical properties, and characteristic features, at the same level of detail as incompressible turbulence in conventional viscous fluids. Here we present such a phenomenology that captures in simple terms many known features and regimes of quantum turbulence, in both the limit of zero temperature and the temperature range of two-fluid behavior.

LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all modern web browsers and mobile devices. LiteMol suite is a combination of data delivery services (CoordinateServer and DensityServer), compression format (BinaryCIF), and a molecular viewer (LiteMol Viewer). The LiteMol suite is integrated into Protein Data Bank in Europe (PDBe) and other life science web applications (e.g., UniProt, Ensemble, SIB, and CNRS services), it is freely available at https://litemol.org , and its source code is available via GitHub. LiteMol suite provides advanced functionality (annotations and their visualization, powerful selection features), and this chapter will describe their use for visual inspection of protein structures.

LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all modern web browsers and mobile devices. LiteMol suite is a combination of data delivery services (CoordinateServer and DensityServer), compression format (BinaryCIF), and a molecular viewer (LiteMol Viewer). The LiteMol suite is integrated into Protein Data Bank in Europe (PDBe) and other life science web applications (e.g., UniProt, Ensemble, SIB, and CNRS services), it is freely available at https://litemol.org , and its source code is available via GitHub. LiteMol suite provides advanced functionality (annotations and their visualization, powerful selection features), and this chapter will describe their use for visual inspection of protein structures.

Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability.This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.

We have performed a study of quantum turbulence generated in oscillatory counterflow as a continuation of previous experiments on various channel flows of superfluid helium, in the form of coflow, thermal DC counterflow and pure superflow. We have investigated its development, steady state properties and temporal decay, as well as the effect of the resonant mode used to generate the turbulence at three different temperatures, 1.45 K, 1.65 K and 1.83 K. The attenuation of low amplitude second sound, orientated perpendicularly to the long axis of the resonator, was used to determine the amount of quantized vortices created. One of the main goals of this work was to characterize the critical parameters for the onset of instabilities in oscillatory counterflow and to determine their values. Decay measurements of the vortex line density allowed us to distinguish between Vinen-type and Kolmogorov- type decays of quantum turbulence.

Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability. This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.

Selected benzo[c]phenathridine alkaloids were biotransformed using rat liver microsomes and identified by liquid chromatography and mass spectrometry. While the metabolites of commercially available sanguinarine and chelerythrine have been studied in detail, data about the metabolism of the minor alkaloids remained unknown. Reactions involved in transformation include single and/or double O-demethylation, demethylenation, reduction, and hydroxylation. Two metabolites, when isolated, purified and tested for toxicity, were found to be less toxic than the original compounds.

The principal aim of this Thesis is the construction of a cryogenic setup for the investigation of quantum turbulence in superfluid helium (He II) using microresonators and a to perform a study of the transition to turbulence in oscillatory flow of He II in the temperature range from 2.170 K down to 1.293 K. We have designed and constructed a setup consisting of a superconducting vibrating microwire and a so-called fountain pump, and, after initial testing and characterization, used it to probe the instabilities occurring in the flow of He II. Specifically, we were interested in the origin of the instabilities in the flow around the microwire and in the question whether they originate mostly from classical-like flow of the normal component, as is often the case with the well-known tuning forks, or whether they are related to the generation of quantized vortices in the superfluid component of He II. To distinguish between these two types of instabilities, we have derived from the Navier-Stokes equations scaling laws related to drag forces in classical oscillatory flow, which we have applied to the normal component of superfluid helium. This also enabled us to verify the validity of the high-frequency limit of oscillatory flow for the case of the microwire. Finally, we have examined the capability of the...

Composition and organization of secondary structure elements (SSEs), such as alpha-helices and beta-sheets, are characteristic for protein families and they participate in formation of protein fold. They are however often influenced by the sequence variability and ligand binding. For this reason, identification of similarities and differences between SSEs can help us in the analysis of individual proteins within a protein family. To utilize the SSEs for research of individual protein families, we need to have the SSEs easily and automatically intercomparable within one protein family. Specifically, the corresponding SSEs should have the same name (annotation) and there should be a transparent schema of their localization in the protein structures. Unfortunately, SSE annotations are still performed mainly manually and universal automatic approach to assign SSE names is not available yet. Moreover, current methods focused on 2D visualization of SSEs (e.g., PROMOTIF, Pro-origami, HERA) do not consider information about real distances of SSEs. Therefore, even when two proteins from the same family differ only slightly, their SSE 2D diagrams can be totally different. For this reason, we developed a tool set which can perform SSE annotation and 2D visualization in such a way that structural information is kept. Applicability of this approach is shown in a case study focused on cytochromes P450. This protein family of drug-metabolizing enzymes has currently available more than 750 structures from about 30 organisms and each cytochrome P450 contains more than 20 SSEs for which there is a stable annotation used through the community. Our approach can be further extended to other protein structural families, which will allow family-wide SSE annotations and comparisons in a simple visual manner.