525 research outputs found

    MS-GWaM: A 3-dimensional transient gravity wave parametrization for atmospheric models

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    Parametrizations for internal gravity waves in atmospheric models are traditionally subject to a number of simplifications. Most notably, they rely on both neglecting wave propagation and advection in the horizontal direction (single-column assumption) and an instantaneous balance in the vertical direction (steady-state assumption). While these simplifications are well justified to cover some essential dynamic effects and keep the computational effort small it has been shown that both mechanisms are potentially significant. In particular, the recently introduced Multiscale Gravity Wave Model (MS-GWaM) successfully applied ray-tracing methods in a novel type of transient but columnar internal gravity wave parameterization (MS-GWaM-1D). We extend this concept to a three-dimensional version of the parameterization (MS-GWaM-3D) to simulate subgrid-scale non-orographic internal gravity waves. The resulting global wave model -- implemented into the weather-forecast and climate code ICON -- contains three-dimensional transient propagation with accurate flux calculations, a latitude-dependent background source, and convectively generated waves. MS-GWaM-3D helps reproducing expected temperature and wind patterns in the mesopause region in the climatological zonal mean state and thus proves a viable IGW parameterization. Analyzing the global wave action budget, we find that horizontal wave propagation is as important as vertical wave propagation. The corresponding wave refraction includes previously missing but well-known effects such as wave refraction into the polar jet streams. On a global scale, three-dimensional wave refraction leads to a horizontal flow-dependent redistribution of waves such that the structures of the zonal mean wave drag and consequently the zonal mean winds are modified.Comment: 39 pages, 9 figures; This Work has been submitted to the Journal of Atmospheric Sciences. Copyright in this Work may be transferred without further notic

    Hemodynamic Quantifications By Contrast-Enhanced Ultrasound:From In-Vitro Modelling To Clinical Validation

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    Efficient algorithms for simulation and analysis of many-body systems

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    This thesis introduces methods to efficiently generate and analyze time series data of many-body systems. While we have a strong focus on biomolecular processes, the presented methods can also be applied more generally. Due to limitations of microscope resolution in both space and time, biomolecular processes are especially hard to observe experimentally. Computer models offer an opportunity to work around these limitations. However, as these models are bound by computational effort, careful selection of the model as well as its efficient implementation play a fundamental role in their successful sampling and/or estimation. Especially for high levels of resolution, computer simulations can produce vast amounts of high-dimensional data and in general it is not straightforward to visualize, let alone to identify the relevant features and processes. To this end, we cover tools for projecting time series data onto important processes, finding over time geometrically stable features in observable space, and identifying governing dynamics. We introduce the novel software library deeptime with two main goals: (1) making methods which were developed in different communities (such as molecular dynamics and fluid dynamics) accessible to a broad user base by implementing them in a general-purpose way, and (2) providing an easy to install, extend, and maintain library by employing a high degree of modularity and introducing as few hard dependencies as possible. We demonstrate and compare the capabilities of the provided methods based on numerical examples. Subsequently, the particle-based reaction-diffusion simulation software package ReaDDy2 is introduced. It can simulate dynamics which are more complicated than what is usually analyzed with the methods available in deeptime. It is a significantly more efficient, feature-rich, flexible, and user-friendly version of its predecessor ReaDDy. As such, it enables---at the simulation model's resolution---the possibility to study larger systems and to cover longer timescales. In particular, ReaDDy2 is capable of modeling complex processes featuring particle crowding, space exclusion, association and dissociation events, dynamic formation and dissolution of particle geometries on a mesoscopic scale. The validity of the ReaDDy2 model is asserted by several numerical studies which are compared to analytically obtained results, simulations from other packages, or literature data. Finally, we present reactive SINDy, a method that can detect reaction networks from concentration curves of chemical species. It extends the SINDy method---contained in deeptime---by introducing coupling terms over a system of ordinary differential equations in an ansatz reaction space. As such, it transforms an ordinary linear regression problem to a linear tensor regression. The method employs a sparsity-promoting regularization which leads to especially simple and interpretable models. We show in biologically motivated example systems that the method is indeed capable of detecting the correct underlying reaction dynamics and that the sparsity regularization plays a key role in pruning otherwise spuriously detected reactions

    SuperCDMS HVeV Run 2 Low-Mass Dark Matter Search, Highly Multiplexed Phonon-Mediated Particle Detector with Kinetic Inductance Detector, and the Blackbody Radiation in Cryogenic Experiments

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    There is ample evidence of dark matter (DM), a phenomenon responsible for ≈ 85% of the matter content of the Universe that cannot be explained by the Standard Model (SM). One of the most compelling hypotheses is that DM consists of beyond-SM particle(s) that are nonluminous and nonbaryonic. So far, numerous efforts have been made to search for particle DM, and yet none has yielded an unambiguous observation of DM particles. We present in Chapter 2 the SuperCDMS HVeV Run 2 experiment, where we search for DM in the mass ranges of 0.5--10⁴ MeV/c² for the electron-recoil DM and 1.2--50 eV/c² for the dark photon and the Axion-like particle (ALP). SuperCDMS utilizes cryogenic crystals as detectors to search for DM interaction with the crystal atoms. The interaction is detected in the form of recoil energy mediated by phonons. In the HVeV project, we look for electron recoil, where we enhance the signal by the Neganov-Trofimov-Luke effect under high-voltage biases. The technique enabled us to detect quantized e⁻h⁺ creation at a 3% ionization energy resolution. Our work is the first DM search analysis considering charge trapping and impact ionization effects for solid-state detectors. We report our results as upper limits for the assumed particle models as functions of DM mass. Our results exclude the DM-electron scattering cross section, the dark photon kinetic mixing parameter, and the ALP axioelectric coupling above 8.4 x 10⁻³⁴ cm², 3.3 x 10⁻¹⁴, and 1.0 x 10⁻⁹, respectively. Currently every SuperCDMS detector is equipped with a few phonon sensors based on the transition-edge sensor (TES) technology. In order to improve phonon-mediated particle detectors' background rejection performance, we are developing highly multiplexed detectors utilizing kinetic inductance detectors (KIDs) as phonon sensors. This work is detailed in chapter 3 and chapter 4. We have improved our previous KID and readout line designs, which enabled us to produce our first ø3" detector with 80 phonon sensors. The detector yielded a frequency placement accuracy of 0.07%, indicating our capability of implementing hundreds of phonon sensors in a typical SuperCDMS-style detector. We detail our fabrication technique for simultaneously employing Al and Nb for the KID circuit. We explain our signal model that includes extracting the RF signal, calibrating the RF signal into pair-breaking energy, and then the pulse detection. We summarize our noise condition and develop models for different noise sources. We combine the signal and the noise models to be an energy resolution model for KID-based phonon-mediated detectors. From this model, we propose strategies to further improve future detectors' energy resolution and introduce our ongoing implementations. Blackbody (BB) radiation is one of the plausible background sources responsible for the low-energy background currently preventing low-threshold DM experiments to search for lower DM mass ranges. In Chapter 5, we present our study for such background for cryogenic experiments. We have developed physical models and, based on the models, simulation tools for BB radiation propagation as photons or waves. We have also developed a theoretical model for BB photons' interaction with semiconductor impurities, which is one of the possible channels for generating the leakage current background in SuperCDMS-style detectors. We have planned for an experiment to calibrate our simulation and leakage current generation model. For the experiment, we have developed a specialized ``mesh TES'' photon detector inspired by cosmic microwave background experiments. We present its sensitivity model, the radiation source developed for the calibration, and the general plan of the experiment.</p

    Cloud condensation nuclei concentrations from spaceborne lidar measurements – Methodology and validation

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    Aerosol-cloud interactions are the most uncertain component of the anthropogenic radiative forcing. A substantial part of this uncertainty comes from the limitations of currently used spaceborne CCN proxies that (i) are column integrated and do not guarantee vertical co-location of aerosols and clouds, (ii) have retrieval issues over land, and (iii) do not account for aerosol hygroscopicity. A possible solution to overcome these limitations is to use height-resolved measurements of the spaceborne lidar aboard the CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation) satellite. This thesis presents a novel CCN retrieval algorithm based on Optical Modelling of CALIPSO Aerosol Microphysics (OMCAM) that is designed particularly for CALIPSO lidar measurements, along with its validation with airborne and surface in-situ measurements. \noindent OMCAM uses a set of normalized size distributions from the CALIPSO aerosol model and modifies them to reproduce the CALIPSO measured aerosol extinction coefficient. It then uses the modified size distribution and aerosol type-specific CCN parameterizations to estimate the number concentration of CCN (nCCN) at different supersaturations. The algorithm accounts for aerosol hygroscopicity by using the kappa parametrization. Sensitivity studies suggest that the uncertainty associated with the output nCCN may range between a factor of 2 and 3. OMCAM-estimated aerosol number concentrations (ANCs) and nCCN are validated using temporally and spatially co-located in-situ measurements. In the first part of validation, the airborne observations collected during the Atmospheric Tomography (ATom) mission are used. It is found that the OMCAM estimates of ANCs are in good agreement with the in-situ measurements with a correlation coefficient of 0.82, an RMSE of 247.2 cm-3, and a bias of 44.4 cm-3. The agreement holds for all aerosol types, except for marine aerosols, in which the OMCAM estimates are about an order of magnitude smaller than the in-situ measurements. An update of the marine model in OMCAM improve the agreement significantly. In the second part of validation, the OMCAM-estimated ANC and nCCN are compared to measurements from seven surface in-situ stations covering a variety of aerosol environments. The OMCAM-estimated monthly nCCN are found to be in reasonable agreement with the in-situ measurements with a 39 % normalized mean bias and 71 % normalized mean error. Combining the validation studies, the algorithm outputs are found to be consistent with the co-located in-situ measurements at different altitude ranges over both land and ocean. Such an agreement has not yet been achieved for spaceborne-derived CCN concentrations and demonstrates the potential of using CALIPSO lidar measurements for inferring global 3D climatologies of CCN concentrations related to different aerosol types.:1 Introduction . . . . . . . . . . . . . . . 1 1.1 Background: Aerosols in the climate system . . . . . . . . . . . . . . . . . 1 1.1.1 Aerosol-induced effective radiative forcing . . . . . . . . . . . . . . 3 1.1.2 Significance of aerosol-cloud interactions . . . . . . . . . . . . . . . 3 1.2 Observation-based ACI studies . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2.1 In-situ studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2.2 Spaceborne studies . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Spaceborne CCN proxies and their limitations . . . . . . . . . . . . . . . . 8 1.4 CCN concentrations from lidars . . . . . . . . . . . . . . . . . . . . . . . . 10 1.5 Objective: CCN from spaceborne lidar . . . . . . . . . . . . . . . . . . . . 11 2 Paper 1: Estimating cloud condensation nuclei concentrations from CALIPSO lidar measurements . . . . . . . . . . . . . . . 15 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 2.2 Data and retrievals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.2.1 CALIPSO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.2.2 MOPSMAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.2.3 POLIPHON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.3 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 2.3.1 Aerosol size distribution . . . . . . . . . . . . . . . . . . . . . . . . 20 2.3.2 Aerosol hygroscopicity . . . . . . . . . . . . . . . . . . . . . . . . . 23 2.3.3 CCN parameterizations . . . . . . . . . . . . . . . . . . . . . . . . 23 2.3.4 Application of OMCAM to CALIPSO retrieval . . . . . . . . . . . 23 2.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.4.1 Sensitivity analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.4.2 Comparison with POLIPHON . . . . . . . . . . . . . . . . . . . . . 30 2.4.3 Case study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 2.5 Summary and conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3 Paper 2: Evaluation of aerosol number concentrations from CALIPSO with ATom airborne in situ measurements . . . . . . . . . . . . . . . 39 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3.2 Data, retrievals, and methods . . . . . . . . . . . . . . . . . . . . . . . . . 42 3.2.1 ATom 3.2.2 CALIOP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 3.2.3 Aerosol number concentration from CALIOP . . . . . . . . . . . . 44 3.2.4 Data matching and comparison . . . . . . . . . . . . . . . . . . . . 48 3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.3.1 Example cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.3.2 General findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 3.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 3.6 Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 4 Paper 3: Assessment of CALIOP-derived CCN concentrations by in situ surface measurements . . . . . . . . . . . . . . . 65 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 4.2 Data and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 4.2.1 In situ observations . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 4.2.2 CALIOP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 4.2.3 Comparison Methodology . . . . . . . . . . . . . . . . . . . . . . . 71 4.3 Comparison of CCN Concentrations . . . . . . . . . . . . . . . . . . . . . . 73 4.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 5 Summary and conclusions . . . . . . . . . . . . . . . 79 6 Outlook . . . . . . . . . . . . . . . 83 References . . . . . . . . . . . . . . . 88 List of Abbreviations . . . . . . . . . . . . . . . 107 List of Variables . . . . . . . . . . . . . . . 109 List of Figures . . . . . . . . . . . . . . . 111 List of Tables . . . . . . . . . . . . . . . 113 A List of Publications . . . . . . . . . . . . . . . 115 B Acknowledgements . . . . . . . . . . . . . . . 11

    X-ray polarization properties of partially ionized equatorial obscurers around accreting compact objects

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    We present the expected X-ray polarization signal resulting from distant reprocessing material around black holes. Using a central isotropic power-law emission at the center of the simulated model, we add distant equatorial and axially symmetric media that are covering the central accreting sources. We include partial ionization and partial transparency effects, and the impact of various polarization and steepness of the primary radiation spectrum. The results are obtained with the Monte Carlo code STOKES that considers both line and continuum processes and computes the effects of scattering and absorption inside static homogenous wedge-shaped and elliptical toroidal structures, varying in relative size, composition and distance to the source. We provide first order estimates for parsec-scale reprocessing in Compton-thin and Compton-thick active galactic nuclei, as well as winds around accreting stellar-mass compact objects, for observer's inclinations above and below the grazing angle. The resulting reprocessed polarization can reach tens of % with either parallel or perpendicular orientation with respect to the axis of symmetry, depending on subtle details of the geometry, density and ionization structure. We also show how principal parameters constrained from X-ray spectroscopy or polarimetry in other wavelengths can lift the shown degeneracies in X-ray polarization. We provide an application example of the broad modelling discussion by revisiting the recent IXPE 2-8 keV X-ray polarimetric observation of the accreting stellar-mass black hole in Cygnus X-3 from the perspective of partial transparency and ionization of the obscuring outflows.Comment: 22 pages, 21 figures. Submitted to MNRA

    Elucidating the Structure and Regulatory Interactions of the HOTAIR Non-Coding RNA and the Bacterial RNase P. Holoenzyme

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    RNA structures and RNA-protein interactions are studied as potential drug targets, biomarkers in cancer, and can be administered as vaccines. The cancer associated HOTAIR (HOX transcript antisense RNA) exists in higher vertebrates and interacts with chromatin remodeling enzymes. We examined the thermodynamic folding properties and structural propensity of the exonic regions of HOTAIR using biophysical methods and NMR spectroscopy. Different exons of HOTAIR contain variable degrees of structural heterogeneity. We identify one exonic region, exon 4, that adopts a stable and compact fold under low magnesium concentrations. Close agreement of NMR spectroscopy and chemical probing confirm conserved base pair interactions within helix 10 of exon 4 of the human HOTAIR long non-coding RNA (lncRNA). Unlike HOTAIR, the ribonuclease P (RNase P) exists in bacteria, archaea and eukarya. RNase P is a universal RNA-protein endonuclease that catalyzes 5′ precursor-tRNA (ptRNA) processing. Protein concentration and temperature dependent NMR studies were performed on a thermostable RNase P protein from Thermatoga maritima to understand its oligomerization properties. The identification of a monomeric P protein conformer from NMR relaxation data and chemical shift information provided new insight into the conformational dynamics of the P protein. Taken together, local structural changes of the P protein and the 5′ leader RNA facilitate optimal substrate alignment and catalytic activation of the RNase P holoenzyme. As RNase P is an essential enzyme in life, knowledge of the structural differences between pathogenic bacterial and human RNase P may help in the development of new antibiotic therapeutics that target RNase P. The enzyme activity of Mycobacterium tuberculosis RNase P was examined through 32P radioactivity assays, and multidimensional 2D/3D NMR spectroscopy was implemented to study the solution structure of the M. tuberculosis RNase P protein. A comparative analysis of the pathogenic and non-pathogenic RNase P proteins brings important structural insight into the development of antibiotics that target tuberculosis RNase P

    Serial sectioning block-face imaging of post-mortem human brain

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    No current imaging technology can directly and without significant distortion visualize the defining microscopic features of the human brain. Ex vivo histological techniques yield exquisite planar images, but the cutting, mounting and staining they require induce slice-specific distortions, introducing cross-slice differences that prohibit true 3D analysis. Clearing techniques have proven difficult to apply to large blocks of human tissue and cause dramatic distortions as well. Thus, we have only a poor understanding of human brain structures that occur at a scale of 1–100 μm, in which neurons are organized into functional cohorts. To date, mesoscopic features which are critical components of this spatial context, have only been quantified in studies of 2D histologic images acquired in a small number of subjects and/or over a small region of the brain, typically in the coronal orientation, implying that features that are oblique or orthogonal to the coronal plane are difficult to properly analyze. A serial sectioning optical coherence tomography (OCT) imaging infrastructure will be developed and utilized to obtain images of cyto- and myelo-architectural features and microvasculature network of post-mortem human brain tissue. Our imaging infrastructure integrates vibratome with imaging head along with pre and post processing algorithms to construct volumetric OCT images of cubic centimeters of brain tissue blocks. Imaging is performed on tissue block-face prior to sectioning, which preserves the 3D information. Serial sections cut from the block can be subsequently treated with multiplexed histological staining of multiple molecular markers that will facilitate cellular classification or imaged with high-resolution transmission birefringence microscope. The successful completion of this imaging infrastructure enables the automated reconstruction of undistorted volume of human tissue brain blocks and permits studying the pathological alternations arising from diseases. Specifically, the mesoscopic and microscopic pathological alternations, as well as the optical properties and cortical morphological alternations of the dorsolateral prefrontal cortical region of two difference neurodegeneration diseases, Chronic Traumatic Encephalopathy (CTE) and Alzheimer’s Disease (AD), were evaluated using this imaging infrastructure
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