Jan Åström

Stiffness of compressed fiber mats

We investigate, using an analytical and a numerical model, the in-plane stiffness of fiber mats. A mat is modeled by randomly depositing thin linear-elastic fibers on top of each other under the influence of an external pressure. The external pressure has the effect of bending the fibers over each other. The fibers are assumed rigidly bonded at contacts. For a low external pressure the stiffness of the mat deviates from that of its two-dimensional projection only by a geometrical factor, and the effective Poisson contraction is close to zero. For higher pressures, stiffness is governed by two competing effects and a maximum appears in the stiffness. The effective Poisson ratio is clearly negative in this range. An approximative analytical description is developed for the stiffness of mats formed under low external pressure. The stiffness is given as a function of only a few parameters: the degree of bonding, the dimensions of the fibers, the elastic constants of the fiber material, and the density of fibers.

Crumpling of a Stiff Tethered Membrane

A first-principles numerical model for crumpling of a stiff tethered membrane is introduced. This model displays wrinkles, ridge formation, ridge collapse, and initiation of stiffness divergence. The amplitude and wavelength of the wrinkles and the scaling exponent of the stiffness divergence are consistent with both theory and experiment. Close to the stiffness divergence further buckling is hindered by the nonzero thickness of the membrane, and its elastic behavior becomes similar to that of dry granular media. No change in the distribution of contact forces can be observed at the crossover, implying that the network of ridges is then simultaneously a granular force-chain network.

A discrete-element model for viscoelastic deformation and fracture of glacial ice

a b s t r a c t A discrete-element model was developed to study the behavior of viscoelastic materials that are allowed to fracture. Applicable to many materials, the main objective of this analysis was to develop a model specifically for ice dynamics. A realistic model of glacial ice must include elasticity, brittle fracture and slow viscous deformations. Here the model is described in detail and tested with several benchmark simulations. The model was used to simulate various ice-specific applications with resulting flow rates that were compatible with Glens law, and produced under fragmentation fragment-size distributions that agreed with the known analytical and experimental results.

Aster formation and rupture transition in semi-flexible fiber networks with mobile cross-linkers

Fibrous active network structures whose properties are regulated by motor proteins, or simply motors, are fundamental to life. Here, a full elastic and three dimensional model for such networks and motors is presented. The effects of surface anchoring are accounted for and we demonstrate that for unidirectional motors two basic contractile phases emerge in these systems. The transition is governed by a single parameter (τb/τc) which is the ratio of the breaking strain (τb) and the motility limiting strain (τc) of the motors. For τb/τc ≲ 2 and clamped boundaries, the network ruptures and formation of local asters occurs with a high density of motors at the centre and the fibers radially spanning out. This phase displays contraction strain during the formation of asters but the network stress is relaxed once the asters have emerged, demonstrating that the formation of aster-like structures provides a mechanism for stress relaxation. For 2.7 ≲ τb/τc the network remains intact, but reaches a force equilibrium with a high contraction strain in the case of clamped boundaries. Between these two limits the network is partly ruptured. Experimental measurements (e.g. J. T. Nishizaka, H. Miyata, H. Yoshikawa, S. Ishiwata and K. Kinosita Jr., Nature, 1995, 377, 251 and J. F. Finer, R. M. Simmons, J. A. Spudich, Nature, 1994, 368, 113) indicate that actin filament and myosin motors interact with τb/τc ≈ 2.7 which is right at the limit of motor induced fracture for a random network, indicating that e.g. a cytoskeleton with active myosin is susceptible to rupture. This is perhaps not a coincidence and may well be an important factor contributing to cellular dynamics. In the case of free boundaries the network collapses onto one single aster. We also show that the distribution of energy on the motors is a power-law, below the motility limit energy, with the exponent −0.5.

Preparing scientific application software for exascale computing

Many of the most widely used scientifc application software of today were developed largely during a time when the typical amount of compute cores was calculated in tens or hundreds. Within a not too distant future the number of cores will be calculated in at least hundreds of thousands or even millions. A European collaboration group CRESTA has recently been working on a set of renowned scientific software to investigate and develop these codes towards the realm of exascale computing. The codes are ELMFIRE, GROMACS, IFS, HemeLB, NEK5000, and OpenFOAM. This paper contains a summary of the strategies for their development towards exascale and results achieved during the first year of the collaboration project.

Myosin motor mediated contraction is enough to produce cytokinesis in the absence of polymerisation

Actin filament networks play an active role in cytokinesis of eukaryotic cells. These networks, linked mainly by myosin, are concentrated below the cell membrane forming a spherical supporting shell. During cytokinesis, this network is modified such that a contractile ring is formed along the diameter of the shell. We present a realistic three-dimensional simulation model to study the dynamics of this spherical shell of elastic actin filaments and myosin motors. The results show compelling evidence that this fibre-spring model, with the motors activated in a narrow region around the division plane, is sufficient to reproduce most of the essential mechanics of cytokinesis: A spontaneous formation of a contractile ring, a characteristic filament orientation structure, and realistic cleavage furrow dynamics. These results demonstrate that, though cytokinesis is a highly complex process with large variation in intricate details, the fundamental dynamics are largely generic. In particular, motor mediated contraction of an unstructured filament mesh is sufficient to undergo division without concentrated and directed polymerization in the cleavage zone.

Discrete element simulations of crumpling of thin sheets

Forced crumpling of stiff self-avoiding sheets is studied by discrete element simulations. Simulations display stress condensation and scaling of ridge energy in agreement with theoretical expectations for elastic and frictionless sheets, and extends such behavior to elasto-plastic sheets. Crumpling of ideally elastic and frictionless sheets is compared to that of elasto-plastic sheets and sheets with friction.

CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions

Abstract We present a new open source software package CellSim3D for computer simulations of mechanical aspects (that is, biochemical details are not accounted for) of cell division in three dimensions. It is also possible to use the software in the mode with cell division and growth turned off which allows for simulations of soft colloidal matter. The code is based on a previously introduced two dimensional mechanical model for cell division which is extended to full 3D. CellSim3D is written in C/C++ and CUDA and allows for simulations of 100,000 cells using standard desktop computers. Program summary Program Title: CellSim3D version 1.0 Program Files doi: http://dx.doi.org/10.17632/9ffxhfdtzm.1 Licensing provisions: GPLv2 Programming language: C/C++, CUDA, Python Nature of problem: Mechanical 3-dimensional model for cell division and soft colloidal matter Solution method: Representation of cells as elastic three dimensional spheres with elastic forces, friction, repulsion, attraction and osmotic pressure. Integration of the equations of motion using the velocity-Verlet method from dissipative particle dynamics. Cells with volumes higher than a threshold can divide. Cell division can also be turned off thus allowing for simulations of soft colloidal matter. Additional comments: Software web site: https://github.com/SoftSimu/CellSim3D

Calving glaciers and ice shelves

ABSTRACT Calving, or the release of icebergs from glaciers and floating ice shelves, is an important process transferring mass into the world’s oceans. Calving glaciers and ice sheets make a large contribution to sea-level rise, but large uncertainty remains about future ice sheet response to alternative carbon scenarios. In this review, we summarize recent progress in understanding calving processes and representing them in the models needed to predict future ice sheet evolution and sea-level rise. We focus on two main types of calving models: (1) discrete element models that represent ice as assemblages of particles linked by breakable bonds, which can explicitly simulate fracture and calving processes; and (2) continuum models, in which calving processes are parameterized using simple calving laws. With a series of examples using both synthetic and real-world ice geometries, we show how explicit models are yielding a detailed, process-based understanding of system physics that can be translated into predictive capability via improved calving laws. Graphical Abstract

Applied Parallel and Scientific Computing

Many of the most widely used scientifc application software of today were developed largely during a time when the typical amount of compute cores was calculated in tens or hundreds. Within a not too distant future the number of cores will be calculated in at least hundreds of thousands or even millions. A European collaboration group CRESTA has recently been working on a set of renowned scientific software to investigate and develop these codes towards the realm of exascale computing. The codes are ELMFIRE, GROMACS, IFS, HemeLB, NEK5000, and OpenFOAM. This paper contains a summary of the strategies for their development towards exascale and results achieved during the first year of the collaboration project.