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 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
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Tissue growth kinetics and interface dynamics depend on the properties of the tissue environment and cell-cell interactions. In cellular environments, substrate heterogeneity and geometry arise from ...a variety factors, such as the structure of the extracellular matrix and nutrient concentration. We used the CellSim3D model, a kinetic cell division simulator, to investigate the growth kinetics and interface roughness dynamics of epithelial tissue growth on heterogeneous substrates with varying topologies. The results show that the presence of quenched disorder has a clear effect on the colony morphology and the roughness scaling of the interface in the moving interface regime. In a medium with quenched disorder, the tissue interface has a smaller interface roughness exponent, α, and a larger growth exponent, β. The scaling exponents also depend on the topology of the substrate and cannot be categorized by well-known universality classes.
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3.
Calving glaciers and ice shelves Benn, Douglas I.; Åström, Jan A.
Advances in physics: X,
20/1/1/, Volume:
3, Issue:
1
Journal Article
Peer reviewed
Open access
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.
The universality of interfacial roughness in growing epithelial tissue has remained a controversial issue. Kardar-Parisi-Zhang (KPZ) and molecular beam epitaxy (MBE) universality classes have been ...reported among other behaviors including a total lack of universality. Here, we simulate tissues using the cellsim3d kinetic division model for deformable cells to investigate cell-colony scaling. With seemingly minor model changes, it can reproduce both KPZ- and MBE-like scaling in configurations that mimic the respective experiments. Tissue growth with strong cell-cell adhesion in a linear geometry is KPZ like, while weakly adhesive tissues in a radial geometry are MBE like. This result neutralizes the apparent scaling controversy.
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Tissue topology, in particular proliferating epithelium topology, is remarkably similar between various species. Understanding the mechanisms that result in the observed topologies is needed for ...better insight into the processes governing tissue formation. We present a two-dimensional single-cell based model for cell divisions and tissue growth. The model accounts for cell mechanics and allows cell migration. Cells do not have pre-existing shapes or topologies. Shape changes and local rearrangements occur naturally as a response to the evolving cellular environment and cell-cell interactions. We show that the commonly observed tissue topologies arise spontaneously from this model. We consider different cellular rearrangements that accompany tissue growth and study their effects on tissue topology.
A two-dimensional single-cell based model for cell divisions and tissue growth.
We investigate morphologies of proliferating cellular tissues using a numerical simulation model for mechanical cell division and migration in two dimensions. The model is applied to a bimodal ...mixture consisting of stiff cells with a low growth potential and soft cells with a high growth potential; cancer cells are typically considered to be softer than healthy cells. In an even mixture, the soft cells develop into a tissue matrix and the stiff cells into a dendritelike network structure. When soft cells are placed inside a tissue consisting of stiff cells (to model cancer growth), the soft cells develop into a fast-growing tumorlike structure that gradually evacuates the stiff cell matrix. The model also demonstrates (1) how soft cells orient themselves in the direction of the largest effective stiffness as predicted by the theory of Bischofs and Schwarz Proc. Natl. Acad. Sci. USA 100, 9274 (2003)PNASA60027-842410.1073/pnas.1233544100 and (2) that the orientation and force generation continue a few cell rows behind the soft-stiff interface. With increasing intercell friction, tumor growth slows down, and cell death occurs. The contact force distribution between cells is demonstrated to be highly sensitive to cell type mixtures and cell-cell interactions, which indicates that local mechanical forces can be useful as a regulator of tissue formation. The results shed light on established experimental data.
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A major challenge within material science is the proper modeling of force transmission through fragmenting materials under compression. A particularly demanding material is sea ice, which on small ...scales is an anisotropic material with quasibrittle characteristics under failure. Here we use the particle-based model HiDEM and laboratory-scale experiments on saline ice to develop a material model for fragmenting ice. The material behavior of the HiDEM model-ice, and the experiments are compatible on force transmission and fragmentation if: (i) the typical HiDEM glacier-scale particle size of meters is brought down to millimeters corresponding to the grain size of the laboratory ice, (ii) the often used HiDEM lattice structure is replaced by a planar random structure with an anisotropy in the direction normal to the randomized plane, and (iii) the instant tensile and bending failure criterion, used in HiDEM on glacier scale, is replaced by a cohesive softening failure potential for energy dissipation. The main outcomes of this exercise is that many of the, more or less, traditional ice modeling schemes are proven to be incomplete. In particular, local crushing of ice is not valid as a generic failure mode for fragmented ice under compression. Rather, shear failure, as described by Mohr-Coulomb theory is demonstrated to be the dominant failure mode.
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Considerable experimental and theoretical research has been dedicated to understanding the connection between the biochemical activity of cells and their mechanical environment. This is exemplified ...by the common structures of developing epithelial cells between various species and the decay of cell population growth rate over time. We study these two phenomena in a system of simulated cells with identical mechanical properties, and growth factors in both epithelial and 3D configurations embedded in viscous fluid. We demonstrate that the increase in the density of cellular systems and the consequential crowding of cells by their neighbors are crucial factors in causing the decay of tissue growth rate. We also show that tissue structure can be reproduced by a purely mechanical model with a more faithful treatment of inter-membrane interactions. Finally, we also show that, assuming all other factors constant, growth, and final structure depends on inter-membrane and medium friction coefficients. Of these two, the latter has a stronger influence on slowing down growth and disrupting structure.
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We discuss quantum annealing of the two-dimensional transverse-field Ising model on a D-Wave device, encoded on L×L lattices with L≤32. Analyzing the residual energy and deviation from maximal ...magnetization in the final classical state, we find an optimal L dependent annealing rate v for which the two quantities are minimized. The results are well described by a phenomenological model with two powers of v and L-dependent prefactors to describe the competing effects of reduced quantum fluctuations (for which we see evidence of the Kibble-Zurek mechanism) and increasing noise impact when v is lowered. The same scaling form also describes results of numerical solutions of a transverse-field Ising model with the spins coupled to noise sources. We explain why the optimal annealing time is much longer than the coherence time of the individual qubits.
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The marine-terminating outlet in Basin 3, Austfonna ice cap, has been accelerating since the mid-1990s. Stepwise multi-annual acceleration associated with seasonal summer speed-up events was observed ...before the outlet entered the basin-wide surge in autumn 2012. We used multiple numerical models to explore hydrologic activation mechanisms for the surge behaviour. A continuum ice dynamic model was used to invert basal friction coefficient distributions using the control method and observed surface velocity data between April 2012 and July 2014. This has provided input to a discrete element model capable of simulating individual crevasses, with the aim of finding locations where meltwater entered the glacier during the summer and reached the bed. The possible flow paths of surface meltwater reaching the glacier bed as well as those of meltwater produced at the bed were calculated according to the gradient of the hydraulic potential.
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