arXiv subjects

C. Wagner

Publications and source records attributed to C. Wagner.

At least 19 recordsLinked to original sources

arXiv2025

Temperature and pressure reconstruction in turbulent Rayleigh-B\'enard convection by Lagrangian velocities using PINN

Velocity, pressure, and temperature are the key variables for understanding thermal convection, and measuring them all is a complex task. In this paper, we demonstrate a method to reconstruct temperature and pressure fields based on given Lagrangian velocity data. A physics-informed neural network (PINN) based on a multilayer perceptron architecture and a periodic sine activation function is used to reconstruct both the temperature and the pressure for two cases of turbulent Rayleigh-B\'enard convection (Pr = 6.9, Ra = $10^9$). The first dataset is generated with DNS and it includes Lagrangian velocity data of 150000 tracer particles. The second contains a PTV experiment with the same system parameters in a water-filled cubic cell, and we observed about 50000 active particle tracks per time step with the open-source framework proPTV. A realistic temperature and pressure field could be reconstructed in both cases, which underlines the importance of PINNs also in the context of experimental data. In the case of the DNS, the reconstructed temperature and pressure fields show a 90\% correlation over all particles when directly validated against the ground truth. Thus, the proposed method, in combination with particle tracking velocimetry, is able to provide velocity, temperature, and pressure fields in convective flows even in the hard turbulence regime. The PINN used in this paper is compatible with proPTV and is part of an open source project. It is available on request at https://github.com/DLR-AS-BOA.

physics.flu-dyn↗

arXiv2024

Influence of erythrocyte density on aggregability as a marker of cell age: Dissociation dynamics in extensional flow

Blood rheology and microcirculation are strongly influenced by red blood cell (RBC) aggregation. The aggregability of RBCs can vary significantly due to factors such as their mechanical and membrane surface properties, which are affected by cell aging in vivo. In this study, we investigate RBC aggregability as a function of their density, a marker of cell age and mechanical properties, by separating RBCs from healthy donors into different density fractions using Percoll density gradient centrifugation. We examine the dissociation rates of aggregates in a controlled medium supplemented with Dextran, employing an extensional flow technique based on hyperbolic microfluidic constrictions and image analysis, assisted by a convolutional neural network (CNN). In contrast to other techniques, our microfluidic experimental approach highlights the behavior of RBC aggregates in dynamic flow conditions relevant to microcirculation. Our results demonstrate that aggregate dissociation is strongly correlated with cell density and that aggregates formed from the denser fractions of RBCs are significantly more robust than those from the average cell population. This study provides insight into the effect of RBC aging in vivo on their mechanical properties and aggregability, underscoring the importance of further exploration of RBC aggregation in the context of cellular senescence and its potential implications for hemodynamics. Additionally, it suggests that this technique can complement existing methods for improved evaluation of RBC aggregability in health and disease.

physics.bio-ph↗

arXiv2021

Lingering Dynamics in Microvascular Blood Flow

The microvascular networks in the body of vertebrates consist of the smallest vessels such as arterioles, capillaries, and venules. The flow of RBCs through these networks ensures the gas exchange in as well as the transport of nutrients to the tissues. Any alterations in this blood flow may have severe implications on the health state. Since the vessels in these networks obey dimensions similar to the diameter of RBCs, dynamic effects on the cellular scale play a key role. The steady progression in the numerical modeling of RBCs, even in complex networks, has led to novel findings in the field of hemodynamics, especially concerning the impact and the dynamics of lingering events, when a cell meets a branch of the network. However, these results are yet to be matched by a detailed analysis of the lingering experiments in vivo. To quantify this lingering effect in in vivo experiments, this study analyzes branching vessels in the microvasculature of Syrian golden hamsters via intravital microscopy and the use of an implanted dorsal skinfold chamber. It also presents a detailed analysis of these lingering effects of cells at the apex of bifurcating vessels, affecting the temporal distribution of cell-free areas of blood flow in the branches, even causing a partial blockage in severe cases.

physics.bio-ph↗

arXiv2020

Artificial neural networks for 3D cell shape recognition from confocal images

We present a dual-stage neural network architecture for analyzing fine shape details from microscopy recordings in 3D. The system, tested on red blood cells, uses training data from both healthy donors and patients with a congenital blood disease. Characteristic shape features are revealed from the spherical harmonics spectrum of each cell and are automatically processed to create a reproducible and unbiased shape recognition and classification for diagnostic and theragnostic use.

q-bio.QM↗

arXiv2018

Anti-margination of microparticles and platelets in the vicinity of branching vessels

We investigate the margination of microparticles/platelets in blood flow through complex geometries typical for in vivo vessel networks: a vessel confluence and a bifurcation. Using 3D Lattice-Boltzmann simulations, we confirm that behind the confluence of two vessels a cell-free layer devoid of red blood cells develops in the channel center. Despite its small size of roughly one micrometer, this central cell-free layer persists for up to 100 $μ$m after the confluence. Most importantly, we show from simulations that this layer also contains a significant amount of microparticles/platelets and validate this result by in vivo microscopy in mouce venules. At bifurcations, however, a similar effect does not appear and margination is largely unaffected by the geometry. This anti-margination towards the vessel center after a confluence may explain in vivo observations by Woldhuis et al. [Am. J. Physiol. 262, H1217 (1992)] where platelet concentrations near the vessel wall are seen to be much higher on the arteriolar side (containing bifurcations) than on the venular side (containing confluences) of the vascular system.

physics.bio-ph↗

arXiv2017

3D tomography of cells in micro-channels

We combine confocal imaging, microfluidics and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far been limited to steady specimen, we overcome this restriction and present a method to access the 3D shape of moving objects. The key of our principle is a tilted arrangement of the micro-channel with respect to the focal plane of the microscope. This forces cells to traverse the focal plane in an inclined manner. As a consequence, individual layers of passing cells are recorded which can then be assembled to obtain the volumetric representation. The full 3D information allows for a detailed comparisons with theoretical and numerical predictions unfeasible with e.g.\ 2D imaging. Our technique is exemplified by studying flowing red blood cells in a micro-channel reflecting the conditions prevailing in the microvasculature. We observe two very different types of shapes: `croissants' and `slippers'. Additionally, we perform 3D numerical simulations of our experiment to confirm the observations. Since 3D confocal imaging of cells in flow has not yet been realized, we see high potential in the field of flow cytometry where cell classification thus far mostly relies on 1D scattering and fluorescence signals.

physics.flu-dyn↗

arXiv2017

Interaction between carbon nanotubes and metals: Electronic properties, stability, and sensing

The interactions between carbon nanotubes (CNTs) and metal adatoms as well as metal contacts are studied by means of ab initio electronic structure calculations. We show that the electronic properties of a semiconducting (8,4) CNT can be modified by small amounts of Pd adatoms. Such a decoration conserves the piezoelectric properties of the CNT. Besides the electronic influence, the stability of a single adatom, which is of big importance for future technology applications, is investigated as well. We find only small energy barriers for the diffusion of a Pd adatom on the CNT surface. Thus, single Pd adatoms will be mobile at room temperature. Finally we present results for the interaction between a metallic (6,0) CNT and metal surfaces. Binding energies and distances for Al, Cu, Pd, Ag, Pt, and Au are discussed and compared, showing remarkable agreement between the interaction of single metal atoms and metal surfaces with CNTs.

cond-mat.mes-hall↗

arXiv2017

Nanomechanics of CNTs for Sensor Application

A nanoscopic simulation for an acceleration sensor is aimed based on the piezoresistive effect of carbon nanotubes (CNTs). Therefore, a compact model is built from density functional theory (DFT), compared with results of molecular dynamics (MD) that describes the mechanics of carbon nanotubes in a parameterized way. The results for the interesting kind of CNTs [(6,3) and (7,4)] within the two approaches agree in a satisfying way, when DFT-calculations are performed with atomic configurations obtained by MD geometry optimization. Geometry optimization yields the Poisson ratio for CNTs. Thus, values from MD and DFT are compared. The simulation finally aims the modeling of the conductive behavior of CNTs when strain is applied, but this needs further verification. Here, we present the prediction of the tight binding model for suitable CNTs.

cond-mat.mes-hall↗

arXiv2017

Theoretical investigation of in situ k-restore processes for damaged ultra-low-k dielectrics

Ultra-low-k (ULK) materials are essential for today's production of integrated circuits (ICs). However, during the manufacturing process the ULK's low dielectric constant (k-value) increases due to the replacement of hydrophobic species with hydrophilic groups. We investigate the use of plasma enhanced fragmented silylation precursors to repair this damage. The fragmentation of the silylation precursors octamethylcyclotetrasiloxane (OMCTS) and bis(dimethylamino)-dimethylsilane (DMADMS) and their possible repair reactions are studied using density functional theory (DFT) and molecular dynamics (MD) simulations.

physics.chem-ph↗

arXiv2017

Theoretical investigation of an in situ k-restore process for damaged ultra-low-k materials based on plasma enhanced fragmentation

We present theoretical investigations of a k-restore process for damaged pourous ultra-low-k (ULK) materials. The process is based on plasma enhanced fragmented silylation precursors to replace k-value damaging, polar Si-OH and Si-H bonds by k-value lowering Si-CH$_{3}$ bonds. We employ density functional theory (DFT) to determine the favored fragments of silylation precursors and show the successful repair of damaged bonds on our model system. This model system consists of a small set of ULK-fragments which represent various damaged states of ULK materials. Our approach provides a fast scanning method for a wide variety of possible repair reactions. Further, we show that oxygen containing fragments are required to repair Si-H bonds and fragments with dangling Si-bonds are most effective to repair polar Si-OH bonds.

cond-mat.mes-hall↗

arXiv2017

Ab-initio Study of the Trimethylaluminum Atomic Layer Deposition Process on Carbon Nanotubes - An Alternative Initial Step

Electronic applications of carbon nanotubes (CNTs) require the deposition of dielectric films on the tubes while conserving their excellent electronic properties. In our density functional theory study we use the trimethylaluminum (TMA) atomic layer deposition (ALD) as a model process for a CNT-functionalization. Since this functionalization relies on the presence of OH-groups, the CNTs are exposed to a water or oxygen pre-treatment. We show that only CNTs with a single-vacancy defect are able to react with H$_{2}$O or O$_{2}$. Further, the defect is preferably saturated by oxygen. This leaves the CNT without the necessary hydroxyl groups for the first TMA addition. Therefore, we propose an alternative initial step after which a classical TMA ALD process can be performed on the CNT.

cond-mat.mes-hall↗

arXiv2017

DFT investigations of the piezoresistive effect of carbon nanotubes for sensor application

We investigate the piezoresistive effect of carbon nanotubes (CNTs) within density functional theory (DFT) aiming at application-relevant CNTs. CNTs are excellent candidates for the usage in nano-electromechanical sensors (NEMS) due to their small band gap at zero strain leading to a finite resistivity at room temperature. The application of strain induces a band gap-opening leading to a tremendous change in the resistivity. DFT with the LDA approximation yields reasonable results for pure carbon systems like CNTs and is applied to calculate the electronic structure of experimentally relevant CNTs. For the transport part, a simple ballistic transport model based on the band gap is used. We compare our DFT results for the band gaps of strained CNTs to results of tight binding (TB) models. By introducing a scaling factor of $\sqrt{2}$, an excellent agreement of the the DFT data with TB model published by Yang et al. [1] is obtained.

cond-mat.mes-hall↗

arXiv2017

Empirical transport model of strained CNT transistors used for sensor applications

We present an empirical model for the nearballistic transport in carbon nanotube (CNT) transistors used as strain sensors. This model describes the intrinsic effect of strain on the transport in CNTs by taking into account phonon scattering and thermally activated charge carriers. As this model relies on a semiempirical description of the electronic bands, different levels of electronic structure calculations can be used as input. The results show that the electronic structure of strained single-walled CNTs with a radius larger than 0.7nm can be described by a fully analytical model in the sensing regime. For CNTs with smaller diameter, parameterized data from electronic structure calculations can be used for the model. Depending on the type of CNTs, the conductance can vary by several orders of magnitude when strain is applied, which is consistent with the current literature. Further, we demonstrate the tuning of the sensor by an external gate which allows shifting the signal amplitude and the strain sensitivity. These parameters have to be balanced to get good sensing properties. Due to its basically analytical nature, the transport model can be formulated as a compact model for circuit simulations.

cond-mat.mes-hall↗

arXiv2017

Bright 5 - 85 MeV Compton gamma-ray pulses from GeV laser-plasma accelerator and plasma mirror

We convert a GeV laser-plasma electron accelerator into a compact femtosecond-pulsed $γ$-ray source by inserting a $100 μ$m-thick glass plate $\sim3$ cm after the accelerator exit. With near-unity reliability, and requiring only crude alignment, this glass plasma mirror retro-reflected spent drive laser pulses (photon energy $\hbarω_L = 1.17$ eV) with $>50\%$ efficiency back onto trailing electrons (peak Lorentz factor $1000 < γ_e < 4400$), creating an optical undulator that generated $\sim10^8 γ$-ray photons with sub-mrad divergence, estimated peak brilliance $\sim10^{21}$ photons/s/mm$^2$/mrad$^2$/$0.1\%$ bandwidth and negligible bremsstrahlung background. The $γ$-ray photon energy $E_γ= 4γ_e^2 \hbarω_L$, inferred from the measured $γ_e$ on each shot, peaked from 5 to 85 MeV, spanning a range otherwise available with comparable brilliance only from large-scale GeV-linac-based high-intensity $γ$-ray sources.

physics.acc-ph↗

arXiv2017

A foam model highlights the differences of the macro- and microrheology of respiratory horse mucus

Native horse mucus is characterized with micro- and macrorheology and compared to hydroxyethylcellulose (HEC) gel as a model. Both systems show comparable viscoelastic properties on the microscale and for the HEC the macrorheology is in good agreement with the microrheology. For the mucus, the viscoelastic moduli on the macroscale are several orders of magnitude larger than on the microscale. Large amplitude oscillatory shear experiments show that the mucus responds nonlinearly at much smaller deformations than HEC. This behavior fosters the assumption that the mucus has a foam like structure on the microscale compared to the typical mesh like structure of the HEC, a model that is supported by cryogenic-scanning-electron-microscopy (CSEM) images. These images allow also to determine the relative amount of volume that is occupied by the pores and the scaffold. Consequently, we can estimate the elastic modulus of the scaffold. We conclude that this particular foam like microstructure should be considered as a key factor for the transport of particulate matter which plays a central role in mucus function with respect to particle penetration. The mesh properties composed of very different components are responsible for macroscopic and microscopic behavior being part of particles fate after landing.

cond-mat.soft↗

arXiv2017

In-phase and anti-phase flagellar synchronization by basal coupling

We present a theory of flagellar synchronization in the green alga Chlamydomonas, using full treatment of flagellar hydrodynamics. We find that two recently proposed synchronization mechanisms, basal coupling and flagellar waveform compliance, stabilize anti-phase synchronization if operative in isolation. Their nonlinear superposition, however, stabilizes in-phase synchronization as observed in experiments. Our theory predicts different synchronization dynamics in fluids of increased viscosity or external flow, suggesting a non-invasive way to control synchronization by hydrodynamic coupling.

q-bio.CB↗

arXiv2014

Computation of the Halo Mass Function Using Physical Collapse Parameters: Application to Non-Standard Cosmologies

In this article we compare the halo mass function predicted by the excursion set theory with a drifting diffusive barrier against the results of N-body simulations for several cosmological models. This includes the standard LCDM case for a large range of halo masses, models with different types of primordial non-Gaussianity, and the Ratra-Peebles quintessence model of Dark Energy. We show that in all those cosmological scenarios, the abundance of dark matter halos can be described by a drifting diffusive barrier, where the two parameters describing the barrier have physical content. In the case of the Gaussian LCDM, the statistics are precise enough to actually predict those parameters at different redshifts from the initial conditions. Furthermore, we found that the stochasticity in the barrier is nonnegligible making the simple deterministic spherical collapse model a bad approximation even at very high halo masses. We also show that using the standard excursion set approach with a barrier inspired by peak patches leads to inconsistent predictions of the halo mass function.

astro-ph.CO↗

arXiv2014

The plasma protein fibrinogen stabilizes clusters of red blood cells in microcapillary flows

The supply of oxygen and nutrients and the disposal of metabolic waste in the organs depend strongly on how blood, especially red blood cells, flow through the microvascular network. Macromolecular plasma proteins such as fibrinogen cause red blood cells to form large aggregates, called rouleaux, which are usually assumed to be disaggregated in the circulation due to the shear forces present in bulk flow. This leads to the assumption that rouleaux formation is only relevant in the venule network and in arterioles at low shear rates or stasis. Thanks to an excellent agreement between combined experimental and numerical approaches, we show that despite the large shear rates present in microcapillaries, the presence of either fibrinogen or the synthetic polymer dextran leads to an enhanced formation of robust clusters of red blood cells, even at haematocrits as low as 1%. Robust aggregates are shown to exist in microcapillaries even for fibrinogen concentrations within the healthy physiological range. These persistent aggregates should strongly affect cell distribution and blood perfusion in the microvasculature, with putative implications for blood disorders even within apparently asymptomatic subjects.

physics.bio-ph↗