arXiv subjects

Dag Kristian Dysthe

Publications and source records attributed to Dag Kristian Dysthe.

14 recordsLinked to original sources

arXiv2026

From OpenSPIM to FlowSPIM: Enhancing the versatility of a light sheet microscope through an iterative design process

Light sheet microscopy is ideal for the 3D imaging of large biological specimens, yet systematic documentation on adapting microscope designs to diverse experimental requirements remains limited. We present the iterative process used to design and build a modular light-sheet microscope and adapt it to different sample types and experimental conditions. Starting from a stripped-down OpenSPIM platform, we gradually make our microscope more versatile by implementing new hardware, such as additional laser channels and optical filters, and new protocols for sample handling. In its final iteration, FlowSPIM is a new flow-based incubation technique for 3D tissue culture.

physics.optics↗

arXiv2025

Spontaneous elongation of 3D gastruloids from local cell polarity alignment

Gastruloids are 3D stem cell aggregate models for early embryogenesis that provide a unique platform to study how collective cell dynamics drive tissue symmetry breaking and axial elongation. Using 3D light sheet imaging, we show that a pulse of Chiron, a Wnt activator, induces coherent alignment of cell polarity during elongation. While nuclear elongation occurs with or without treatment, only Chiron-treated gastruloids exhibit quasi-long-range alignment of nuclear axes, linking cell polarity coherence to tissue-scale remodeling. A minimal physical model of polarized cells, incorporating alignment-dependent torques and polarity-mediated adhesion, reproduces symmetry breaking and elongation, demonstrating that local cell polarity alignment alone can drive tissue-scale convergence-extension flows.

physics.bio-ph↗

arXiv2024

Role of tissue fluidization and topological defects in epithelial tubulogenesis

Cellular rearrangements, as primary sources of tissue fluidization, facilitate topological transitions during tissue morphogenesis. We study the role of intrinsic cell properties such as cell polarity and cell-cell adhesion in shaping epithelial tissues using a minimal model of interacting polarized cells. The presence of a vortex in the cell polarization poses the topological constraint that induces an inwards migration with the formation of a conical shape. Local rearrangements at the tip of the cone lead to the onset of tube formation. Switching between collective migration and structural rearrangements is key for balancing the contrasting tendencies, such as the tissue rigidity needed to preserve shape and the tissue fluidity allowing for topological transitions during tissue morphogenesis.

physics.bio-ph↗

arXiv2022

Crystal growth in confinement

The growth of crystals confined in porous or cellular materials is ubiquitous in Nature and industry. Confinement affects the formation of biominerals in living organisms, of minerals in the Earth's crust and of salt crystals damaging porous limestone monuments, and is also used to control the growth of artificial crystals. However, the mechanisms by which confinement alters crystal shapes and growth rates are still not elucidated. Based on novel \textit{in situ} optical observations of (001) surfaces of NaClO$_3$ and CaCO$_3$ crystals at nanometric distances from a glass substrate, we demonstrate that new molecular layers can nucleate homogeneously and propagate without interruption even when in contact with other solids, raising the macroscopic crystal above them. Confined growth is governed by the peculiar dynamics of these molecular layers controlled by the two-dimensional transport of mass through the liquid film from the edges to the center of the contact, with distinctive features such as skewed dislocation spirals, kinetic localization of nucleation in the vicinity of the contact edge, and directed instabilities. Confined growth morphologies can be predicted from the values of three main dimensionless parameters.

cond-mat.mtrl-sci↗

arXiv2021

Limits to crystallization pressure

Crystallization pressure drives deformation and damage in monuments, buildings and the Earth's crust. Even though the phenomenon has been known for 170 years there is no agreement between theoretical calculations of the maximum attainable pressure and that found experimentally. We have therefore developed a novel experimental technique to image the nano-confined crystallization process while controlling the pressure and applied it to calcite. The results show that displacement by crystallization pressure is arrested at pressures well below the thermodynamic limit. We use existing molecular dynamics simulations and atomic force microscopy data to construct a robust model of the disjoining pressure in this system and thereby calculate the absolute distance between the surfaces. Based on the high resolution experiments and modelling we formulate a novel mechanism for the transition between damage and adhesion by crystallization that may find application in Earth and materials sciences and in conservation of cultural heritage.

cond-mat.mtrl-sci↗

arXiv2019

Nucleation in Confinement Generates Long-range Repulsion between Rough Calcite Surfaces

Fluid-induced alteration of rocks and mineral-based materials often starts at confined mineral interfaces where nm-thick water films can persist even at high overburden pressures and at low vapor pressures. These films enable transport of reactants and affect forces acting between mineral surfaces. However, the feedback between the surface forces and reactivity of confined solids is not fully understood. We used the surface forces apparatus (SFA) to follow surface reactivity in confinement and measure nm-range forces between two rough calcite surfaces in NaCl, CaCl$_2$, or MgCl$_2$ solutions with ionic strength of 0.01, 0.1 or 1 M. We observed long-range repulsion that could not be explained by changes in calcite surface roughness, surface damage, or by electrostatic or hydration repulsion, but was correlated with precipitation events which started at $μ$m-thick separations. We observed a poorly crystalline or amorphous precipitate that formed in the confined solution. This liquid-like precipitate did not undergo any spontaneous ripening into larger crystals, which suggested that confinement prevented its dehydration. Nucleation was significantly postponed in the presence of Mg$^{2+}$. The long-range repulsion generated by nucleation between confined mineral surfaces can have a crucial influence on the evolution of the microstructure and therefore the macroscopic strength of rocks and materials.

cond-mat.mtrl-sci↗

arXiv2018

Microfluidic control of nucleation and growth of calcite

The nucleation and growth of calcite is an important research in scientific and industrial field. Both the macroscopic and microscopic observation of calcite growth have been reported. Now, with the development of microfluidic device, we could focus the nucleation and growth of one single calcite. By changing the flow rate of fluid, the concentration of fluid is controlled. We introduced a new method to study calcite growth in situ and measured the growth rate of calcite in microfluidic channel.

physics.chem-ph↗

arXiv2018

Cavity formation in confined growing crystals

Growing crystals form a cavity when placed against a wall. The birth of the cavity is observed both by optical microscopy of sodium chlorate crystals (NaClO$_3$) growing in the vicinity of a glass surface, and in simulations with a thin film model. The cavity appears when growth cannot be maintained in the center of the contact region due to an insufficient supply of growth units through the liquid film between the crystal and the wall. We obtain a non-equilibrium morphology diagram characterizing the conditions under which a cavity appears. Cavity formation is a generic phenomenon at the origin of the formation of growth rims observed in many experiments, and is a source of complexity for the morphology of growing crystals in natural environments. Our results also provide restrictions for the conditions under which compact crystals can grow in confinement.

cond-mat.other↗

arXiv2014

A 4D synchrotron X-ray tomography study of the formation of hydrocarbon migration pathways in heated organic-rich shale

Recovery of oil from oil shales and the natural primary migration of hydrocarbons are closely related processes that have received renewed interests in recent years because of the ever tightening supply of conventional hydrocarbons and the growing production of hydrocarbons from low permeability tight rocks. Quantitative models for conversion of kerogen into oil and gas and the timing of hydrocarbon generation have been well documented. However, lack of consensus about the kinetics of hydrocarbon formation in source rocks, expulsion timing and how the resulting hydrocarbons escape from or are retained in the source rocks motivates further investigation. In particular, many mechanisms for the transport of hydrocarbons from the source rocks in which they are generated into adjacent rocks with higher permeabilities and smaller capillary entry pressures have been proposed, and a better understanding of this complex process (primary migration) is needed. To characterize these processes it is imperative to use the latest technological advances. In this study, it is shown how insights into hydrocarbon migration in source rocks can be obtained by using sequential high resolution synchrotron X-ray tomography. Three-dimensional (3D) images of several immature "shale" samples were constructed at resolutions close to 5 micrometers. This is sufficient to resolve the source rock structure down to the grain level, but very fine grained silt particles, clay particles and colloids cannot be resolved. Samples used in this investigation came from the R-8 unit in the upper part of the Green River Shale, which is organic rich, varved, lacustrine marl formed in Eocene Lake Uinta, United States of America. One Green River Shale sample was heated in-situ up to 400°C as X-ray tomography images were recorded. The other samples were scanned before and after heating at 400°C. During the heating phase, the organic matter was decomposed, and gas was released. Gas expulsion from the low permeability shales was coupled with formation of microcracks. The main technical difficulty was numerical extraction of microcracks that have apertures in the 5 to 30 micrometer range (with 5 micrometers being the resolution limit) from a large 3D volume of X-ray attenuation data. The main goal of the work presented here is to develop a methodology to process these 3D data and image the cracks. This methodology is based on several levels of spatial filtering and automatic recognition of connected domains. Supportive petrographic and thermogravimetric data were an important complement to this study. An investigation of the strain field using two-dimensional image correlation analyses was also performed. As one application of the four-dimensional (4D, space + time) microtomography and the developed workflow, we show that fluid generation was accompanied by crack formation. Under different conditions, in the subsurface, this might provide paths for primary migration.

physics.geo-ph↗

arXiv2012

4D imaging of fracturing in organic-rich shales during heating

To better understand the mechanisms of fracture pattern development and fluid escape in low permeability rocks, we performed time-resolved in situ X-ray tomography imaging to investigate the processes that occur during the slow heating (from 60\degree; to 400\degree;C) of organic-rich Green River shale. At about 350\degree;C cracks nucleated in the sample, and as the temperature continued to increase, these cracks propagated parallel to shale bedding and coalesced, thus cutting across the sample. Thermogravimetry and gas chromatography revealed that the fracturing occurring at ~350\degree;C was associated with significant mass loss and release of light hydrocarbons generated by the decomposition of immature organic matter. Kerogen decomposition is thought to cause an internal pressure build up sufficient to form cracks in the shale, thus providing pathways for the outgoing hydrocarbons. We show that a 2D numerical model based on this idea qualitatively reproduces the experimentally observed dynamics of crack nucleation, growth and coalescence, as well as the irregular outlines of the cracks. Our results provide a new description of fracture pattern formation in low permeability shales.

physics.geo-ph↗

arXiv2010

Role of friction-induced torque in stick-slip motion

We present a minimal quasistatic 1D model describing the kinematics of the transition from static friction to stick-slip motion of a linear elastic block on a rigid plane. We show how the kinematics of both the precursors to frictional sliding and the periodic stick-slip motion are controlled by the amount of friction-induced torque at the interface. Our model provides a general framework to understand and relate a series of recent experimental observations, in particular the nucleation location of micro-slip instabilities and the build up of an asymmetric field of real contact area.

physics.class-ph↗

arXiv2010

The mechanism of porosity formation during solvent-mediated phase transformations

Solvent-mediated solid-solid phase transformations often result in the formation of a porous medium, which may be stable on long time scales or undergo ripening and consolidation. We have studied replace- ment processes in the KBr-KCl-H2O system using both in situ and ex situ experiments. The replacement of a KBr crystal by a K(Br,Cl) solid solution in the presence of an aqueous solution is facilitated by the gen- eration of a surprisingly stable, highly anisotropic and connected pore structure that pervades the product phase. This pore structure ensures efficient solute transport from the bulk solution to the reacting KBr and K(Br,Cl) surfaces. The compositional profile of the K(Br,Cl) solid solu- tion exhibits striking discontinuities across disc-like cavities in the product phase. Similar transformation mechanisms are probably important in con- trolling phase transformation processes and rates in a variety of natural and man-made systems.

physics.chem-ph↗

arXiv2005

Compaction dynamics in ductile granular media

Ductile compaction is common in many natural systems, but the temporal evolution of such systems is rarely studied. We observe surprising oscillations in the weight measured at the bottom of a self-compacting ensemble of ductile grains. The oscillations develop during the first ten hours of the experiment, and usually persist through the length of an experiment (one week). The weight oscillations are connected to the grain--wall contacts, and are directly correlated with the observed strain evolution and the dynamics of grain--wall contacts during the compaction. Here, we present the experimental results and characteristic time constants of the system, and discuss possible reasons for the measured weight oscillations.

cond-mat.soft↗

arXiv2005

Structure of plastically compacting granular packings

The developing structure in systems of compacting ductile grains were studied experimentally in two and three dimensions. In both dimensions, the peaks of the radial distribution function were reduced, broadened, and shifted compared with those observed in hard disk- and sphere systems. The geometrical three--grain configurations contributing to the second peak in the radial distribution function showed few but interesting differences between the initial and final stages of the two dimensional compaction. The evolution of the average coordination number as function of packing fraction is compared with other experimental and numerical results from the literature. We conclude that compaction history is important for the evolution of the structure of compacting granular systems.

cond-mat.soft↗