We perform computer simulations of an agglomeration process for monodisperse and polydisperse systems of spherical particles in a cylindrical container, using a simplified stochastic-hydrodynamic model. We consider a ternary system with three particle types A, B, and C, in which only connections of the type A - B can be forged, while any other connections with particles of the same type or with C-particles are forbidden, and for comparison a binary system with two particle types A and C, in which only connections of the type A - A can be formed. We study the breakdown of the percolation in the agglomeration at the bottom of the cylinder with an increasing fraction of C-particles.

One of the open questions regarding the origin of life is the problem how macromolecules could be created. One possible answer is the existence of autocatalytic sets in which some macromolecules mutually catalyze each other’s formation. This mechanism is theoretically described in the Kauffman model. We introduce and simulate an extension of the Kauffman model, in which ligation and cleavage reactions are spatially separated in different containers connected by diffusion, and provide computational results for instances with and without autocatalytic sets, focusing on the time evolution of the densities of the various molecules. Furthermore, we study the rich behavior of a randomly generated instance containing an autocatalytic metabolism, in which molecules are created by ligation processes and destroyed by cleavage processes and vice versa or generated and destroyed both by ligation processes.

We explain how to optimize the image analysis of mixed clusters of red and green droplets in solvents with various degrees of sharpness, brightness, contrast and density. The circular Hough Transform is highly efficient for separated circles with reasonable background contrast, but not for large amounts of partially overlapping shapes, some of them blurred, as in the images of our dense droplet suspensions. We explain why standard approaches for image improvement fail and present a “shootout” approach, where already detected circles are masked, so that the removal of sharp outlines improves the relative optical quality of the remaining droplets. Nevertheless, for intrinsic reasons, there are limits to the accuracy of data which can be obtained on very dense clusters.

We simulate the movement and agglomeration of oil droplets in water under constraints, using a simplified stochastic-hydrodynamic model. We analyze both local and global properties of the networks formed by the agglomerations of droplets for various system sizes. We focus on the differences of these properties for monodisperse and polydisperse systems of droplets. For the mean degree, we obtain different values for critical exponents.

This study focused on simulating incompressible viscous flow using the finite element method. This study used velocity and pressure as unknowns known as primitive variable formulations. Simulation of incompressible fluid flow poses numerical challenges due to the presence of nonlinear convective terms in Navier-Stokes equations and the incompressible nature of the fluid. If the connection between velocities and pressure is not discretized correctly, the stable and convergent velocities might be gained, but the obtained pressure will be oscillatory. To avoid these difficulties, continuous quadratic and additional cubic bubble functions will be used for the velocity field and linear functions for the pressure field. This kind of discretization satisfies the Ladyzhenskaya-Babuška-Brezzi (LBB) stability condition. Two cases of different Reynolds numbers were used to test the formulation's effectiveness. In the case of Reynolds number 0.12, no vortices were formed, suggesting that the flow is primarily governed by fluid friction, and fluid inertia has minimal effect. In the case of Reynolds number 120, the vortex formation, which is known as Von Kármán vortex street, appeared. These results concluded that the formulation using the finite element method is correct.

We aim at planning and creating specific agglomerations of droplets to study synergic communication using these as programmable units. In this paper, we give an overview of preliminary obstacles for the various research issues, namely of how to create droplets, how to set up droplet agglomerations using DNA technology, how to prepare them for confocal microscopy, how to make a computer see droplets on photos, how to analyze networks of droplets, how to perform simulations mimicking experiments, and how to plan specific agglomerations of droplets.

The development of data science, the increase of computational power, the availability of the internet infrastructure for data exchange and the urgency for an understanding of complex systems require a responsible and ethical use of computational models in science, communication and decision-making. Starting with a discussion of the width of different purposes of computational models, we first investigate the process of model construction as an interplay of theory and experimentation. We emphasise the different aspects of the tension between model variables and experimentally measurable observables. The resolution of this tension is a prerequisite for the responsible use of models and an instrumental part of using models in the scientific processes. We then discuss the impact of models and the responsibility that results from the fact that models support and may also guide experimentation. Further, we investigate the difference between computational modelling in an interdisciplinary science project and computational models as tools in transdisciplinary decision support. We regard the communication of model structures and modelling results as essential; however, this communication cannot happen in a technical manner, but model structures and modelling results must be translated into a “narrative.” We discuss the role of concepts from disciplines such as literary theory, communication science, and cultural studies and the potential gains that a broader approach can obtain. Considering concepts from the liberal arts, we conclude that there is, besides the responsibility of the model author, also a responsibility of the user/reader of the modelling results.

Experimentally, periodically released droplets in systems of widening pipes show clustering. This is surprising, as purely hydrodynamic interactions are repulsive so that agglomeration should be prevented. In the main part of this paper, we investigate the clustering of droplets under the influence of phenomenological hydrostatic forces and some hypothetical attraction. In two appendices, we explain why a direct numerical simulation for this system is rather more difficult (and probably not possible with current methods) than the “simple” geometry would suggest.

Studying the collective behavior of adhesive particles with the discrete element method (DEM) requires well-founded force–displacement relations (force models). While the Johnson–Kendall–Roberts (JKR) theory reliably predicts the dependence of the contact radius a on the force F, it has remained a challenge in this framework to obtain a straightforward force–displacement relation F(δ) with physically meaningful parameters to calculate the force F from the displacement δ. We derive a novel force–displacement relation from the JKR theory as a composition of functions F(δ)=(F∘a∘λ)(δ), with the intermediate functions contact radius a(λ) and effective adhesive contact radius λ(δ). We also analyze contact geometry errors in the Hertz and JKR models, derive the exact contact centroid to accurately calculate contact torques and relative tangential velocities, and propose a smoothed JKR model to avoid discontinuities in force and energy. We find that incorrect torques and relative tangential velocities are obtained when the stiffness quotient is neglected because it affects the exact location of the contact centroid. We also find that contact geometry errors can become non-negligible for nanoparticles due to their large relative contact size. In addition, we show from bouncing ball simulations that the JKR models with a nominal coefficient of restitution derived for the Hertz model result in higher damping and thus reduced actual coefficients of restitution. Our analysis serves as a foundation for contact-mechanics-based force models for DEM simulations of adhesive particles to investigate their collective behavior in the future.

Shapes of constituent particles have a prominent effect on the macroscopic responses of granular assemblies. Clayey minerals often possess a plate-shaped geometry with a large surface-to-volume ratio. It is difficult to model such a geometry with spheres or clusters of spheres in a conventional discrete element method (DEM). In this study, we present a new DEM for plate-shaped particles with a focus on particle geometry and kinematics. The moment of inertia for a general convex plate is given and unit quaternions are adopted to represent the angular degrees of freedom. In addition, the equation of motion for rotation is proposed to be solved in a body-fixed rather than in a space-fixed reference frame. We present simulations of the rotation of a system of plate-shaped particles under the conservation of angular momentum without external torque. The results demonstrate the necessity and importance of enforcing the unity constraint on the quaternions numerically solved from the equation of motion for rotation.

Within the scope of the European Horizon 2020 project ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function , we aim at the development of a chemical compiler governing the three-dimensional arrangement of droplets, which are filled with various chemicals. Neighboring droplets form bilayers with pores which allow chemicals to move from one droplet to its neighbors. With an appropriate three-dimensional configuration of droplets, we can thus enable gradual biochemical reaction schemes for various purposes, e.g., for the production of macromolecules for pharmaceutical purposes. In this paper, we demonstrate with artificial chemistry simulations that the ACDC technology is excellently suitable to maximize the yield of desired reaction products or to minimize the relative output of unwanted side products.

Figure 1: Top: Snapshot of an experimentally found cluster of oil droplets in water recorded with a confocal microscope.Bottom: Final configuration of 2,000 multidisperse particles at the bottom of a cylinder in a computer simulation.

We investigate the avalanches of spherical and non-spherical granular particles inside half-filled rotating drums. The time series of the center of gravity of the particle assemblies are obtained via image analysis and their single-sided amplitude (SSA) spectra are analyzed. The spectra features of this new indicator turn out to be characteristic for the avalanches, in terms of the existence of peaks in the low-frequency range and the decay rate of high frequency components. The SSA spectrum has a peak for the packings of non-spherical particles but not for the spherical particles. The high frequency part is characterized by a power law decay 1/ f a (a > 0) . A 1/ f -decay is found only for the spherical particles. For the packings of cornered particles, the exponents significantly deviate from a = 1. As 1/ f spectra are often associated with self-organized criticality and therefore a scale invariance of the dynamics, we may conclude that there is no scale-invariant structure for granular avalanches. Considering the small number of particles and the regularity of convex particle shapes being used, the spectral features revealed in this study could be utilized for validating particle simulations.

As a follow-up of an earlier work on the numerically exact Coulomb friction in two-dimensional simulations, we present here the relations and implementation for three-dimensional discrete element particles.

In this research, we have improved a relaxation method for triangular meshes intended for finite element fluid simulations which contain discrete element particles. The triangle edges are treated as springs which relax their lengths towards a “better” force equilibrium where the triangles are closer to equilateral shape. The actual kernel is an improved zero order integrator which is able to follow reconfigurations of the particles faster than earlier methods. The improved relaxation allows larger timesteps in the flow simulation and leads to more stable, faster mesh reconfigurations for fast moving particles in the flow. Additionally, this demonstrates how integrators of the same order zero can nevertheless have different convergence speeds towards equilibrium.

For homogeneous systems like classical fluid dynamics and structural mechanics, finite element method (FEM) grid generation has reached a mature state. On the other hand, for multi-physics-problems like fluids with a high density of immersed particles, many researchers may not even be aware of the types of instabilities which may be triggered by unsuitable meshes. We review common types of grid generation, point out previously unrecognised types of instabilities for particles in fluids as well as remedies to obtain particle-fluid simulations with higher stability and fewer redundant degrees of freedom.

Within the context of the European Horizon 2020 project ACDC

We present some work in progress on the development of a probabilistic chemical compiler, being able to make a plan of how to create a three-dimensional agglomeration of artificial hierarchical cellular constructs. These programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory being able to e.g. produce macromolecular medicine on demand, and of scientific investigations, like contributions to questions regarding the origin of life. This paper focuses on one specific issue of developing such a compiler, namely the problem of simulating the experimentally observed spatial transition from an originally one-dimensional lineup of droplets into a three-dimensional, almost spherical arrangement, in which the droplets form a network via bilayers connecting them and in which they are contained within some outer hull. The network created by the bilayers allows the droplets to “communicate” (like agents in a multi agent system) with each other and to exchange chemicals contained within them, thus enabling a complex successive biochemical reaction scheme.

In this paper, we propose a combination of discrete elements for the soil and finite elements for the fluid flow field inside the pore space to simulate the triggering of landslides. We give the details for the implementation of third order finite elements (“P2 with bubble”) together with polygonal discrete elements, which allows the formulation with a minimal number of degrees of freedom to save computer time and memory. We verify the implementation with several standard problems from computational fluid dynamics, as well as the decay of a granular step in a fluid as test case for complex flow.

We present a novel formalism which allows to compute static friction forces in a many body system of non-rigid particles for given normal forces and friction coefficients based on an exact formalism of constraint forces. We derive criteria to discriminate between static and dynamic friction at the contacts based on the phase flow and to evaluate the static friction. Further, we compare the results for this formalism with other approaches. We compute several problems to evaluate the accuracy of the method and discuss and implement approaches for numerical stabilization against creep.