Sebastian Heidenreich

Meso-scale turbulence in living fluids

Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior among the simplest forms of life and is important for fluid mixing and molecular transport on the microscale. The mathematical characterization of turbulence phenomena in active nonequilibrium fluids proves even more difficult than for conventional liquids or gases. It is not known which features of turbulent phases in living matter are universal or system-specific or which generalizations of the Navier–Stokes equations are able to describe them adequately. Here, we combine experiments, particle simulations, and continuum theory to identify the statistical properties of self-sustained meso-scale turbulence in active systems. To study how dimensionality and boundary conditions affect collective bacterial dynamics, we measured energy spectra and structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D geometries. Our experimental results for the bacterial flow statistics agree well with predictions from a minimal model for self-propelled rods, suggesting that at high concentrations the collective motion of the bacteria is dominated by short-range interactions. To provide a basis for future theoretical studies, we propose a minimal continuum model for incompressible bacterial flow. A detailed numerical analysis of the 2D case shows that this theory can reproduce many of the experimentally observed features of self-sustained active turbulence.

Fluid Dynamics of Bacterial Turbulence

Self-sustained turbulent structures have been observed in a wide range of living fluids, yet no quantitative theory exists to explain their properties. We report experiments on active turbulence in highly concentrated 3D suspensions of Bacillus subtilis and compare them with a minimal fourth-order vector-field theory for incompressible bacterial dynamics. Velocimetry of bacteria and surrounding fluid, determined by imaging cells and tracking colloidal tracers, yields consistent results for velocity statistics and correlations over 2 orders of magnitude in kinetic energy, revealing a decrease of fluid memory with increasing swimming activity and linear scaling between kinetic energy and enstrophy. The best-fit model allows for quantitative agreement with experimental data.

Minimal continuum theories of structure formation in dense active fluids

Self-sustained dynamical phases of living matter can exhibit remark- able similarities over a wide range of scales, from mesoscopic vortex structures in microbial suspensions and motility assays of biopolymers to turbulent large- scale instabilities in flocks of birds or schools of fish. Here, we argue that, in many cases, the phenomenology of such active states can be efficiently described in terms of fourth- and higher-order partial differential equations. Structural transitions in these models can be interpreted as Landau-type kinematic transi- tions in Fourier (wavenumber) space, suggesting that microscopically different biological systems can share universal long-wavelength features. This general idea is illustrated through numerical simulations for two classes of continuum models for incompressible active fluids: a Swift-Hohenberg-type scalar field theory, and a minimal vector model that extends the classical Toner-Tu theory and appears to be a promising candidate for the quantitative description of dense bacterial suspensions. We discuss how microscopic symmetry-breaking mech- anisms can enter macroscopic continuum descriptions of collective microbial motion near surfaces, and conclude by outlining future applications.

Modeling of line roughness and its impact on the diffraction intensities and the reconstructed critical dimensions in scatterometry

We investigate the impact of line-edge and line-width roughness (LER, LWR) on the measured diffraction intensities in angular resolved extreme ultraviolet (EUV) scatterometry for a periodic line-space structure designed for EUV lithography. LER and LWR with typical amplitudes of a few nanometers were previously neglected in the course of the profile reconstruction. The two-dimensional (2D) rigorous numerical simulations of the diffraction process for periodic structures are carried out with the finite element method providing a numerical solution of the 2D Helmholtz equation. To model roughness, multiple calculations are performed for domains with large periods, containing many pairs of line and space with stochastically chosen line and space widths. A systematic decrease of the mean efficiencies for higher diffraction orders along with increasing variances is observed and established for different degrees of roughness. In particular, we obtain simple analytical expressions for the bias in the mean efficiencies and the additional uncertainty contribution stemming from the presence of LER and/or LWR. As a consequence this bias can easily be included into the reconstruction model to provide accurate values for the evaluated profile parameters. We resolve the sensitivity of the reconstruction from this bias by using simulated data with LER/LWR perturbed efficiencies for multiple reconstructions. If the scattering efficiencies are bias-corrected, significant improvements are found in the reconstructed bottom and top widths toward the nominal values.

Hydrodynamic length-scale selection in microswimmer suspensions.

A universal characteristic of mesoscale turbulence in active suspensions is the emergence of a typical vortex length scale, distinctly different from the scale invariance of turbulent high-Reynolds number flows. Collective length-scale selection has been observed in bacterial fluids, endothelial tissue, and active colloids, yet the physical origins of this phenomenon remain elusive. Here, we systematically derive an effective fourth-order field theory from a generic microscopic model that allows us to predict the typical vortex size in microswimmer suspensions. Building on a self-consistent closure condition, the derivation shows that the vortex length scale is determined by the competition between local alignment forces, rotational diffusion, and intermediate-range hydrodynamic interactions. Vortex structures found in simulations of the theory agree with recent measurements in Bacillus subtilis suspensions. Moreover, our approach yields an effective viscosity enhancement (reduction), as reported experimentally for puller (pusher) microorganisms.

Improved grating reconstruction by determination of line roughness in extreme ultraviolet scatterometry

The accurate determination of critical dimensions and roughness is necessary to ensure the quality of photoresist masks that are crucial for the operational reliability of electronic components. Scatterometry provides a fast indirect optical nondestructive method for the determination of profile parameters that are obtained from scattered light intensities using inverse methods. We illustrate the effect of line roughness on the reconstruction of grating parameters employing a maximum likelihood scheme. Neglecting line roughness introduces a strong bias in the parameter estimations. Therefore, such roughness has to be included in the mathematical model of the measurement in order to obtain accurate reconstruction results. In addition, the method allows to determine line roughness from scatterometry. The approach is demonstrated for simulated scattering intensities as well as for experimental data of extreme ultraviolet light scatterometry measurements. The results obtained from the experimental data are in agreement with independent atomic force microscopy measurements.

Improved reconstruction of critical dimensions in extreme ultraviolet scatterometry by modeling systematic errors

Scatterometry is a non-imaging indirect optical method that is frequently used to reconstruct the critical dimensions (CD) of periodic nanostructures, e.g. structured wafer surfaces in semiconductor chip production. To solve the inverse problem, we apply a maximum likelihood estimation, introduced in Henn et al (2012 Opt. Express 20 12771–86). Along with the CD values, further relevant quantities like noise parameters of the measured diffraction intensities and the strength of line roughness can be estimated from the measured scattering efficiencies. We investigate three different models for extreme ultraviolet (EUV) scatterometry at an EUV photo mask with increasing complexity by successively including two major sources of systematic errors, namely line roughness and deviations in the multilayer substrate of the EUV mask. Applying the different models to reconstruct the CDs from both simulation and measurement data, we demonstrate the improvements of the reconstruction in terms of simulated and real measurement data. The inclusion of systematic errors in the maximum likelihood approach to the inverse problem leads to a significant reduction of the variances in the estimated CDs implying reduced measurement uncertainty for scatterometry.

Nonlinear rheology of active particle suspensions: insights from an analytical approach.

We consider active suspensions in the isotropic phase subjected to a shear flow. Using a set of extended hydrodynamic equations we derive a variety of analytical expressions for rheological quantities such as shear viscosity and normal stress differences. In agreement to full-blown numerical calculations and experiments we find a shear-thickening or -thinning behavior depending on whether the particles are contractile or extensile. Moreover, our analytical approach predicts that the normal stress differences can change their sign in contrast to passive suspensions.

Numerical simulations of a minimal model for the fluid dynamics of dense bacterial suspensions

Collective behavior is a fascinating phenomenon and ubiquitous in nature. A large variety of complex dynamic structures from swarming to turbulence arise in active particle systems. In recent investigations a set of minimal continuum equations was proposed to model mesoscale bacterial turbulence. Numerical solutions are validated with experimental data of Bacillus subtilis bacteria. In this short paper we present a recently used pseudo-spectral operator splitting method that directly solves the nonlinear equations in the turbulent regime. In two and three spatial dimensions we show the resulting typical velocity and vorticity fields as well as energy spectra to highlight the strong difference between turbulence in ordinary fluids and in bacterial suspensions.

Scatterometry reference standards to improve tool matching and traceability in lithographical nanomanufacturing

High quality scatterometry standard samples have been developed to improve the tool matching between different scatterometry methods and tools as well as with high resolution microscopic methods such as scanning electron microscopy or atomic force microscopy and to support traceable and absolute scatterometric critical dimension metrology in lithographic nanomanufacturing. First samples based on one dimensional Si or on Si3N4 grating targets have been manufactured and characterized for this purpose. The etched gratings have periods down to 50 nm and contain areas of reduced density to enable AFM measurements for comparison. Each sample contains additionally at least one large area scatterometry target suitable for grazing incidence small angle X-ray scattering. We present the current design and the characterization of structure details and the grating quality based on AFM, optical, EUV and X-Ray scatterometry as well as spectroscopic ellipsometry measurements. The final traceable calibration of these standards is currently performed by applying and combining different scatterometric as well as imaging calibration methods. We present first calibration results and discuss the final design and the aimed specifications of the standard samples to face the tough requirements for future technology nodes in lithography.