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42:42 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Computational models of stem cell decisions

Molecular regulation of cell fate decisions underlies health and disease. In my talk, I will present mathematical and statistical models that describe molecular interactions, differentiation decisions, and single cell gene expression. We use these models to infer molecular and cellular properties from biological and biomedical data. For example, in lineage trees of differentiating blood stem cells, we often observe correlated state changes between related cells. Using these correlations and a stochastic model of the differentiation process, we find differentiation events to happen much earlier than previously anticipated. To predict differentiation prospectively, we use a deep neural network trained on image patches from brightfield microscopy and cellular movement. Surprisingly, we can detect lineage choice in blood stem cells up to three generations before conventional molecular lineage markers are observable. Finally, I will present a method for fitting stochastic models to lineage trees. Using a Bayesian inference method, we compare possible models of autoregulation, an important gene regulatory motif in stem cells.>
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
42:48 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Estimation of the mesospheric wind field correlation and structure functions using multistatic specular meteor radars

A method for estimating the three-dimensional mesospheric wind field covariance structure from a sparse set of specular meteor trail echo measurements is described. The measurements consist of one dimensional projections of the vector wind field measured at random points in space and time. The method for estimating the correlation function relies on cross-correlating pairs of Doppler velocity measurements, which are separated in time and space. These measurements can be used to estimate the correlation function of the mesospheric wind field at different spatial and temporal scales. The method is demonstrated using a multistatic specular meteor radar measurement data set that includes ≈105 meteor detections during a 24 hour time period. To validate the method, the results are compared with an established method for estimating horizontal mean wind. The method is also applied for estimation of high resolution temporal, horizontal, and vertical structure of the mesospheric wind. The results are compared with the expected behavior of atmospheric fluctuations at mesospheric altitudes. The temporal correlation function is used to estimate the power spectrum of mesospheric wind, which includes the semidiurnal mode and a strong peak with a 3 hour period. From the horizontal correlation function of the fluctuating wind, we estimate the structure function for the <4 hour fluctuating component and find that the spectral index is close to -5/3, which is consistent with the Kolmogorov distribution of energy within turbulence. The vertical correlation function for the fluctuating component shows that the vertical scale size of <1 hour waves is approximately 10 km for the horizontal wind components. The method described in this study expands the range of spatial and temporal scales of the mesospheric wind covariance structure that can be studied with specular meteor radars, and it may also be applied to other similar sparse and incomplete measurements of random vector fields.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
31:08 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Geothermal reservoir: modeling, simulation and optimization for district heating in hot sedimentary acquires

Geothermal reservoir: modeling, simulation and optimization for district heating in hot sedimentary acquires The performance optimization of a geothermal reservoir depends on the ability of combining available data with the deep understanding of mutually coupled processes over the whole hierarchy of scales, from the pores to the reservoir. These include hydrothermal flows in heterogeneous porous media, mechanical processes, and reactive transport, among others. This work focuses on the geophysical, mathematical, and computational challenges related to the modeling and simulation of geothermal reservoirs, and preliminary results concerning the optimal placement of multi-well systems for geothermal energy production. In this talk, we will overview the results of the ongoing collaboration between LIAG and WIAS, started in the framework of the last MMS days and supported by a MMS Seed Money Grant in 2018. The talk will be jointly presented by A. Caiazzo (WIAS) and E. Meneses (LIAG)
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
27:58 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Anelastic equations as a tool to understand gravity waves and mean-flow effects

Internal gravity waves (GWs) in the atmosphere play a major role in the global circulation of the middle atmosphere (10-100 km height). The mean-flow effects of GWs consist of 1) the momentum deposition (corrected by the Stokes drift of the GWs), 2) the energy deposition (corresponding to the sum of mechanical and thermal dissipation), and 3) the convergence of the GW heat flux. This set of mean-flow effect is obtained from the anelastic equations with sensible heat as prognostic thermodynamc variable. Furthermore, we have to assume the Boussinesq limit for the waves, which means that the vertical wavelength, λz , is assumed to be small against 4π H, where H is the scale height. We show that these anelastic equations yield the usual dispersion and polarization relations for GWs. According to current wisdom, however, these solutions include the case λz ∼ 4π H. New linear theory for by Vadas (2013, J. Geophys. Res.) yields different polarization relations, but confirms the usual dispersion relation. The likely reason for different linear solutions in the case of λz ∼ 4π H is that usual linear theory starts out from the fully compressible equations, and the anelastic limit is calculated separately for the dispersion and polarization relations. In this contribution we present a set of anelastic equations where the Boussinesp limit for perturbations from the reference state is relaxed. We recover the more recent polarization relations for GWs, but obtain a different dispersion relation in the case of λz ∼ 4π H. The mean flow effects from GWs are consistently simulated in a high-resolution circulation model, provided the model is based on the compressible equations and includes a hydrodynamically diffusion schemes. However, a consistent theoretical approach for the mean-flow effects of GWs having large λz is not yet available. According to theory and high-resolution modeling, such GWs occur frequently in the thermosphere.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
27:35 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Non-local effects in the solar dynamo

Model of the solar dynamo hardly reproduce the observations of the solar magnetic field. In the presence of strong magnetic field in a turbulent fully ionized medium, such as the solar interior, temporal and spacial re-correlations can occur. In the frame of mean-field MHD, these can be treated as spacial and temporal non-localities (memory effect). We found that the magnetic buoyancy occurring in the convective solar interior implies a non-linear temporal non-locality. This additional non-linearity leads to solutions that recover the morphological evolution of the solar magnetic field.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
21:56 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Time integration methods for finite element discretizations in weather forecasting

There is a new interest in finite element methods for solving the equations in numerical weather forecasting. In contrast to finite difference and finite volume methods explicit time integration methods are hampered by non-diagonal mass matrices in front of the derivatives. We will compare different mixed finite and discontinuous Galerkin methods for the two-dimensional linear Boussinesq approximation in the context of split-explicit time integration schemes. Especially different lumping procedures are investigated which replaces non-diagonal mass matrices by simple diagonal block-diagonal matrices. These methods are compared with energy conserving implicit Runge-Kutta methods for a non-hydrostatic gravity wave example.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
16:32 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

How Consistent Can We Solve the Tensor Equations of the Dynamic Smagorinsky Model?

The basic idea of the Dynamic Smagorinsky Model (DSM) is the tensor equation that relates the resolved stress terms with the respective Smagorinsky parametrizations. Although there exist for almost 30 years approaches to solve it, they include common practices which are, in my opinion, applied too uncritically. For instance, a stringent derivation of the tensor equation results in an ambiguous formulation involving a divergence operator. A second problem that may cause inconsistencies is the frequently-used extraction of the Smagorinsky parameter from the test filtering. In my presentation, I want to point out some of these issues to obtain a better understanding of the DSM. This may also lead to a reduction of mathematical inconsistencies regarding its solution.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
16:36 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

The roles of imbalances for divergent and rotational modes in atmospheric flows

A three-dimensional general balanced solution to the governing equations of the atmosphere is given. The deviation from this balanced, or inactive, wind solution is called the active wind. For the horizontal components, this active wind is comparable to the ageostrophic wind. The vertical active wind component is similar to the isentropic displacement vertical wind. Transformed governing equations are derived as functions of the active wind components. This is also possible for the vorticity and divergence equations, respectively. It turns out that the classical balance equation is not part of the transformed divergence equation, but reflects the balanced part which had been removed. The terms on the right of the transformed equations can be scrutinized with respect to their effects on the evolution of the atmospheric state. Exemplarily, this is done for an idealized baroclinic wave in a dry atmosphere. The different terms on the right of the transformed equations and the active wind components are visualised and interpreted in their meaning. Most importantly, the newly introduced vertical active wind component allows for an analysis of the vertical motion of isentropes. The baroclinic wave development is discussed with focus on the fronts and the generation or depletion of kinetic energy. The new method allows for a unique separation of gravity waves and vortical modes. This facilitates the analysis of gravity wave generation and propagation from jets and fronts.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
15:33 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Coarse-graining as a technique to reveal sub-grid scale fluxes and test the diffusive assumption.

The limits of model resolution in atmospheric and oceanographic modeling necessitate the use of subgrid parametrizations to account for unresolved processes. The go-to approach is using diffusive parametrizations such as the Dynamical Smagorinsky. In this work use a Coarse-Graining technique to reveal subgrid scale dynamics to test whether or not they do behave according to the diffusive assumption. We find a highly organized and structured turbulent shear production, which leads us to question the underlying assumptions and limits of diffusive parametrizations.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
18:52 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

On the Feasibility of Using Open Source Solvers for the Simulation of Air Flow in a Dairy Building

  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
20:18 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Open Reproducible Research in the Geosciences: Obstacles, Solutions, and Incentives

Many journals today encourage authors to share code and data used in studies, but only a minority enforces it, and rarely give journals guidance on how these materials should be shared. Since computational reproducibility encompasses and naturally follows sharing of the used materials, the adoption by journals is even less developed. The project “Opening reproducible research (o2r)“ designed and implemented solutions to support the publication of reproducible research considering different stakeholders, such as authors, readers, reviewers, and publishers. On top of that, we identified a couple of incentives for authors to make their research accessible, for example, by easily creating interactive (geo)scientific publications. In my talk, I will give a brief overview of the concepts and solutions developed in o2r. On top of that, I will provide insights into our follow-up project o2r2 including concrete cooperations with publishers.>
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
27:20 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

The Julia programming language in applications for electrochemical systems simulation

Julia is a new computer language with multidimensional arrays as first class data types designed for numerical computations. Compared to other languagues with similar purpose (Matlab, python/numpy, R), Julia follows a number of promising paradigms. Julia was designed around a just-in-time compilation strategy which guarantees high single thread performance. At the same time it supports various parallelization approaches (shared/distributed memory, GPU offloading). Programming paradigms like multiple dispatch and reflection provide a high level of expressivity. The talk will give an overview on these features of Julia. Based on first principles of nonequilibrium thermodynamics, at WIAS, a modeling and simulation strategy for electrochemical systems has been developed which accurately accounts for phenomena which are poorly reflected in classical models like finite ion size and constraints, solvation phenomena. These models result in highly nonlinear systems of partial differential equations. The talk presents first steps towards a Julia based implementation of a finite volume bases numerical solution strategy for these systems.>
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
24:58 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

On pressure-robustness, coherent structures and vortex-dominated flows

In vortex-dominated flows at high Reynolds numbers, vortex filaments interact with each other and reveal coherent geometrical structures, possibly persisting over long time scales. The force balance between the material velocity time derivative and the pressure gradient leads to complicated pressure gradients, which have to be handled accurately by the space discretization. It is argued that pressure-robust solvers are needed for long-time simulations of vortex dominated flows at high Reynolds numbers. Numerical benchmarks support the theory.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
30:12 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

First results on two-way coupled model ICONGETM for the Central Baltic Sea

To understand local phenomena over the Baltic Sea such as Coastal Upwelling or Salinity Inversion, we are coupling an atmosphere and ocean model with the Earth System Modelling Framework (ESMF). For the atmosphere, the operational model of the German Weather Service (ICON) is used in a nested limited area mode. The General Estuarine Turbulence Model (GETM) has been chosen as the local ocean model. Typical coupling issues are the different grid schemes of the models and hence, a set and choice of suitable interpolation/regridding methods is required. Within our framework, the state variables (e.g. temperature) and flux data (e.g. heat flux) have to be interpolated from ICON to GETM and vice versa. This presentation will give an overview about the coupling strategy we have applied. Furthermore, the results of first model runs are presented for the Central Baltic Sea. At first, we show results of uncoupled model simulations. Additionally, we will talk about the differences for the coupled model simulations compared to the uncoupled runs.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
22:43 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Reproducibility in Neuroscience - A best practice example

Reproducibility in Neuroscience - A best practice example The last decade has seen intensive discussions on reproducibility in the analysis of neuroimaging experiments. This has lead to efforts in the neuroscience community in various directions, e.g., accessibility of 'minimally processed image and metadata' from large studies for scientific purposes public data archives open data standards open source software and analysis pipelines. This enables, e.g., the development of best practice analysis strategies combination of findings from different studies test of and comparisons with alternative modeling approaches I'll discuss how this fits, as a best practice example, into the current discussions on reproducibility of research and (open) research data.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
14:33 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

Diagnostic wind models in urban air quality modeling

Diagnostic wind models (DWM) may present a feasible choice when full computational fluid dynamics (CFD) is not applicable due to unbearable numerical costs. For selected cases with DWM, it is possible to derive high resolution wind fields in a fraction of time needed to solve the Navier Stokes equations with a comparable quality. DWM solve an optimization problem under the constraint of mass conservation. The initial wind field is interpolated from measurements or a coarse-grid numerical weather prediction model application. Obstacles placed in the wind field are considered by a wake parameterization, which corrects the wind field for the momentum deficit by decreasing the wind speed or reversing the flow in the vicinity of obstacles (Roeckle, 1990, Nelson et al., 2008). The optimization problem is formulated in minimizing the deviation to the modified initial wind field. The solution is a vector potential of the desired wind field, which makes this approach inherently mass conserving. An important application of DWM is in urban air quality modeling, where street-canyon resolving wind fields are required for the realistic computation of emission dispersal.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
27:06 Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP) English 2019

DFT Study of Bifunctional Aliphatic PNP Pincer Catalysts For Hydrogenation - Mechanisms, Scope and Limitation

This short talk presents the computational understanding into the mechanistic aspects of hydrogenation and dehydrogenation as well as transfer hydrogenation reactions of aldehyde, ketone and ester by means of well-defined PNP pincer complexes. The catalytic activity of different catalysts were systematically computed and compared. On the basis of the available experimental results, the scope, limitation and application of computational methods in catalysis were evaluated.
  • Published: 2019
  • Publisher: Weierstraß-Institut für Angewandte Analysis und Stochastik (WIAS), Leibniz-Institut für Atmosphärenphysik (IAP)
  • Language: English
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