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Article: Improving accuracy and efficiency in discrete-continuum karst models

de Rooij, Rob

Environmental earth sciences. 2019 Feb., v. 78, no. 4

2019

Abstract: Discrete-continuum or hybrid models couple one-dimensional conduit flow with the surrounding three-dimensional flow in the fractured rock matrix. The applicability of these models to real karst aquifers is somewhat limited not only because they require ... ...

Abstract	Discrete-continuum or hybrid models couple one-dimensional conduit flow with the surrounding three-dimensional flow in the fractured rock matrix. The applicability of these models to real karst aquifers is somewhat limited not only because they require detailed information about the conduit network, but also these models typically require considerable computational efforts. Moreover, in some models the simulated conduit-matrix exchange fluxes critically depend on a lumped exchange parameter and as such the accuracy of discrete-continuum models can be questionable. This study presents some ideas to improve the accuracy and efficiency of discrete-continuum models. It is shown that a well-index should be used instead of a lumped exchange parameter. It is also illustrated that local grid refinement around the conduits as well as parallel solvers based on domain decomposition can be useful to increase the computational efficiency of discrete-continuum models.
Keywords	aquifers ; karsts ; models
Language	English
Dates of publication	2019-02
Size	p. 115.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	2493699-6
ISSN	1866-6299 ; 1866-6280
ISSN (online)	1866-6299
ISSN	1866-6280
DOI	10.1007/s12665-019-8115-5
Database	NAL-Catalogue (AGRICOLA)

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Article: Physical Biology of Axonal Damage.

de Rooij, Rijk / Kuhl, Ellen

Frontiers in cellular neuroscience

2018 Volume 12, Page(s) 144

Abstract: Excessive physical impacts to the head have direct implications on the structural integrity at the axonal level. Increasing evidence suggests that tau, an intrinsically disordered protein that stabilizes axonal microtubules, plays a critical role in the ... ...

Abstract	Excessive physical impacts to the head have direct implications on the structural integrity at the axonal level. Increasing evidence suggests that tau, an intrinsically disordered protein that stabilizes axonal microtubules, plays a critical role in the physical biology of axonal injury. However, the precise mechanisms of axonal damage remain incompletely understood. Here we propose a biophysical model of the axon to correlate the dynamic behavior of individual tau proteins under external physical forces to the evolution of axonal damage. To propagate damage across the scales, we adopt a consistent three-step strategy: First, we characterize the axonal response to external stretches and stretch rates for varying tau crosslink bond strengths using a discrete axonal damage model. Then, for each combination of stretch rates and bond strengths, we average the axonal force-stretch response of
Language	English
Publishing date	2018-06-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452963-1
ISSN	1662-5102
ISSN	1662-5102
DOI	10.3389/fncel.2018.00144
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Article ; Online: Microtubule Polymerization and Cross-Link Dynamics Explain Axonal Stiffness and Damage.

de Rooij, Rijk / Kuhl, Ellen

Biophysical journal

2018 Volume 114, Issue 1, Page(s) 201–212

Abstract: Axonal damage is a critical indicator for traumatic effects of physical impact to the brain. However, the precise mechanisms of axonal damage are still unclear. Here, we establish a mechanistic and highly dynamic model of the axon to explore the ... ...

Abstract	Axonal damage is a critical indicator for traumatic effects of physical impact to the brain. However, the precise mechanisms of axonal damage are still unclear. Here, we establish a mechanistic and highly dynamic model of the axon to explore the evolution of damage in response to physical forces. Our axon model consists of a bundle of dynamically polymerizing and depolymerizing microtubules connected by dynamically detaching and reattaching cross-links. Although the probability of cross-link attachment depends exclusively on thermal fluctuations, the probability of detachment increases in the presence of physical forces. We systematically probe the landscape of axonal stretch and stretch rate and characterize the overall axonal force, stiffness, and damage as a direct result of the interplay between microtubule and cross-link dynamics. Our simulations reveal that slow loading is dominated by cross-link dynamics, a net reduction of cross-links, and a gradual accumulation of damage, whereas fast loading is dominated by cross-link deformations, a rapid increase in stretch, and an immediate risk of rupture. Microtubule polymerization and depolymerization decrease the overall axonal stiffness, but do not affect the evolution of damage at timescales relevant to axonal failure. Our study explains different failure mechanisms in the axon as emergent properties of microtubule polymerization, cross-link dynamics, and physical forces. We anticipate that our model will provide insight into causal relations by which molecular mechanisms determine the timeline and severity of axon damage after a physical impact to the brain.
MeSH term(s)	Axons/metabolism ; Biomechanical Phenomena ; Mechanical Phenomena ; Microtubules/metabolism ; Models, Biological ; Polymerization
Language	English
Publishing date	2018-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.11.010
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Article: Modeling molecular mechanisms in the axon.

de Rooij, R / Miller, K E / Kuhl, E

Computational mechanics

2016 Volume 59, Issue 3, Page(s) 523–537

Abstract: Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that ... ...

Abstract	Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena-both in isolation and in interaction-to explore emergent cellular-level features under physiological and pathological conditions.
Language	English
Publishing date	2016-12-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1458937-0
ISSN	1432-0924 ; 0178-7675
ISSN (online)	1432-0924
ISSN	0178-7675
DOI	10.1007/s00466-016-1359-y
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Article ; Online: The Shrinking Brain: Cerebral Atrophy Following Traumatic Brain Injury.

Harris, Taylor C / de Rooij, Rijk / Kuhl, Ellen

Annals of biomedical engineering

2018 Volume 47, Issue 9, Page(s) 1941–1959

Abstract: Cerebral atrophy in response to traumatic brain injury is a well-documented phenomenon in both primary investigations and review articles. Recent atrophy studies focus on exploring the region-specific patterns of cerebral atrophy; yet, there is no study ... ...

Abstract	Cerebral atrophy in response to traumatic brain injury is a well-documented phenomenon in both primary investigations and review articles. Recent atrophy studies focus on exploring the region-specific patterns of cerebral atrophy; yet, there is no study that analyzes and synthesizes the emerging atrophy patterns in a single comprehensive review. Here we attempt to fill this gap in our current knowledge by integrating the current literature into a cohesive theory of preferential brain tissue loss and by identifying common risk factors for accelerated atrophy progression. Our review reveals that observations for mild traumatic brain injury remain inconclusive, whereas observations for moderate-to-severe traumatic brain injury converge towards robust patterns: brain tissue loss is on the order of 5% per year, and occurs in the form of generalized atrophy, across the entire brain, or focal atrophy, in specific brain regions. The most common regions of focal atrophy are the thalamus, hippocampus, and cerebellum in gray matter and the corpus callosum, corona radiata, and brainstem in white matter. We illustrate the differences of generalized and focal gray and white matter atrophy on emerging deformation and stress profiles across the whole brain using computational simulation. The characteristic features of our atrophy simulations-a widening of the cortical sulci, a gradual enlargement of the ventricles, and a pronounced cortical thinning-agree well with clinical observations. Understanding region-specific atrophy patterns in response to traumatic brain injury has significant implications in modeling, simulating, and predicting injury outcomes. Computational modeling of brain atrophy could open new strategies for physicians to make informed decisions for whom, how, and when to administer pharmaceutical treatment to manage the chronic loss of brain structure and function.
MeSH term(s)	Atrophy ; Brain/pathology ; Brain Injuries, Traumatic/pathology ; Humans ; Models, Biological
Language	English
Publishing date	2018-10-17
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	185984-5
ISSN	1573-9686 ; 0191-5649 ; 0090-6964
ISSN (online)	1573-9686
ISSN	0191-5649 ; 0090-6964
DOI	10.1007/s10439-018-02148-2
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Article ; Online: Modeling the Axon as an Active Partner with the Growth Cone in Axonal Elongation.

de Rooij, Rijk / Kuhl, Ellen / Miller, Kyle E

Biophysical journal

2018 Volume 115, Issue 9, Page(s) 1783–1795

Abstract: Forces generated by the growth cone are vital for the proper development of the axon and thus brain function. Although recent experiments show that forces are generated along the axon, it is unknown whether the axon plays a direct role in controlling ... ...

Abstract	Forces generated by the growth cone are vital for the proper development of the axon and thus brain function. Although recent experiments show that forces are generated along the axon, it is unknown whether the axon plays a direct role in controlling growth cone advance. Here, we use analytic and finite element modeling of microtubule dynamics and the activity of the molecular motors myosin and dynein to investigate mechanical force balance along the length of the axon and its effects on axonal outgrowth. Our modeling indicates that the paradoxical effects of stabilizing microtubules and the consequences of microtubule disassembly on axonal outgrowth can be explained by changes in the passive and active mechanical properties of axons. Our findings suggest that a full understanding of growth cone motility requires a consideration of the mechanical contributions of the axon. Our study not only has potential applications during neurodevelopment but might also help identify strategies to manipulate and promote axonal regrowth to treat neurodegeneration.
MeSH term(s)	Actins/metabolism ; Axons/metabolism ; Biomechanical Phenomena ; Cytoskeleton/metabolism ; Dyneins/metabolism ; Growth Cones/metabolism ; Mechanical Phenomena ; Microtubules/metabolism ; Models, Neurological ; Myosins/metabolism ; Viscosity ; tau Proteins/metabolism
Chemical Substances	Actins ; tau Proteins ; Myosins (EC 3.6.4.1) ; Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2018-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2018.08.047
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Article: Using Sound Location to Monitor Farrowing in Sows.

van Erp-van der Kooij, Elaine / de Graaf, Lois F / de Kruijff, Dennis A / Pellegrom, Daphne / de Rooij, Renilda / Welters, Nian I T / van Poppel, Jeroen

Animals : an open access journal from MDPI

2023 Volume 13, Issue 22

Abstract: Precision Livestock Farming systems can help pig farmers prevent health and welfare issues around farrowing. Five sows were monitored in two field studies. A Sorama L642V sound camera, visualising sound sources as coloured spots using a 64-microphone ... ...

Abstract	Precision Livestock Farming systems can help pig farmers prevent health and welfare issues around farrowing. Five sows were monitored in two field studies. A Sorama L642V sound camera, visualising sound sources as coloured spots using a 64-microphone array, and a Bascom XD10-4 security camera with a built-in microphone were used in a farrowing unit. Firstly, sound spots were compared with audible sounds, using the Observer XT (Noldus Information Technology), analysing video data at normal speed. This gave many false positives, including visible sound spots without audible sounds. In total, 23 of 50 piglet births were visible, but none were audible. The sow's behaviour changed when farrowing started. One piglet was silently crushed. Secondly, data were analysed at a 10-fold slower speed when comparing sound spots with audible sounds and sow behaviour. This improved results, but accuracy and specificity were still low. When combining audible sound with visible sow behaviour and comparing sound spots with combined sound and behaviour, the accuracy was 91.2%, the error was 8.8%, the sensitivity was 99.6%, and the specificity was 69.7%. We conclude that sound cameras are promising tools, detecting sound more accurately than the human ear. There is potential to use sound cameras to detect the onset of farrowing, but more research is needed to detect piglet births or crushing.
Language	English
Publishing date	2023-11-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani13223538
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Article: Generation of complex karstic conduit networks with a hydrochemical model

de Rooij, Rob / Graham, Wendy

Water resources research. 2017 Aug., v. 53, no. 8

2017

Abstract: In this paper, we present a hydrochemical model that can be used to generate plausible karstic conduit networks that honor what is known about geology, hydrology, and topography of a karst system. To make the model applicable to a range of natural karst ... ...

Abstract	In this paper, we present a hydrochemical model that can be used to generate plausible karstic conduit networks that honor what is known about geology, hydrology, and topography of a karst system. To make the model applicable to a range of natural karst systems, we introduce a flexible and physically realistic flow boundary condition along the land surface. Moreover, whereas comparable existing speleogenesis models use an explicit reactive‐transport scheme, we propose an implicit reactive‐transport scheme to permit a coarser spatial discretization of the conduit cells. An application to a real karst system illustrates that the model can generate a realistic karstic network that reproduces observed hydrologic behavior in terms of current spring flow rates, regional hydraulic head field as well as average groundwater residence times. Our model provides a useful tool to generate ensembles of possible karstic conduit networks that may be used within a stochastic framework to analyze flow and transport prediction uncertainty associated with a lack of knowledge about network geometry.
Keywords	aquifers ; geometry ; groundwater ; hydrochemistry ; karsts ; models ; prediction ; research ; spring ; topography ; uncertainty
Language	English
Dates of publication	2017-08
Size	p. 6993-7011.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	5564-5
ISSN	1944-7973 ; 0043-1397
ISSN (online)	1944-7973
ISSN	0043-1397
DOI	10.1002/2017WR020768
Database	NAL-Catalogue (AGRICOLA)

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Article: Generation of complex karstic conduit networks with a hydrochemical model

de Rooij, Rob / Graham, Wendy

Water resources research

2017 Volume 53, Issue 8, Page(s) 6993

Language	English
Document type	Article
ZDB-ID	5564-5
ISSN	0043-1397
DOI	10.1002/2017WR020768
Database	Current Contents Nutrition, Environment, Agriculture

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Article ; Online: Brain stiffness increases with myelin content.

Weickenmeier, J / de Rooij, R / Budday, S / Steinmann, P / Ovaert, T C / Kuhl, E

Acta biomaterialia

2016 Volume 42, Page(s) 265–272

Abstract: Unlabelled: Brain stiffness plays an important role in neuronal development and disease, but reported stiffness values vary significantly for different species, for different brains, and even for different regions within the same brain. Despite ... ...

Abstract	Unlabelled: Brain stiffness plays an important role in neuronal development and disease, but reported stiffness values vary significantly for different species, for different brains, and even for different regions within the same brain. Despite extensive research throughout the past decade, the mechanistic origin of these stiffness variations remains elusive. Here we show that brain tissue stiffness is correlated to the underlying tissue microstructure and directly proportional to the local myelin content. In 116 indentation tests of six freshly harvested bovine brains, we found that the cerebral stiffnesses of 1.33±0.63kPa in white matter and 0.68±0.20kPa in gray matter were significantly different (p<0.01). Strikingly, while the inter-specimen variation was rather moderate, the minimum and maximum cerebral white matter stiffnesses of 0.59±0.19 kPa and 2.36±0.64kPa in each brain varied by a factor of four on average. To provide a mechanistic interpretation for this variation, we performed a histological characterization of the tested brain regions. We stained the samples with hematoxylin and eosin and luxol fast blue and quantified the local myelin content using image analysis. Interestingly, we found that the cerebral white matter stiffness increased with increasing myelin content, from 0.72kPa at a myelin content of 64-2.45kPa at a myelin content of 89%, with a Pearson correlation coefficient of ρ=0.91 (p<0.01). This direct correlation could have significant neurological implications. During development, our results could help explain why immature, incompletely myelinated brains are softer than mature, myelinated brains and more vulnerable to mechanical insult as evident, for example, in shaken baby syndrome. During demyelinating disease, our findings suggest to use stiffness alterations as clinical markers for demyelination to quantify the onset of disease progression, for example, in multiple sclerosis. Taken together, our study indicates that myelin might play a more important function than previously thought: It not only insulates signal propagation and improves electrical function of single axons, it also provides structural support and mechanical stiffness to the brain as a whole. Statement of significance: Increasing evidence suggests that the mechanical environment of the brain plays an important role in neuronal development and disease. Reported stiffness values vary significantly, but the origin of these variations remains unknown. Here we show that stiffness of our brain is correlated to the underlying tissue microstructure and directly proportional to the local myelin content. Myelin has been discovered in 1854 as an insulating layer around nerve cells to improve electric signal propagation. Our study now shows that it also plays an important mechanical role: Using a combined mechanical characterization and histological characterization, we found that the white matter stiffness increases linearly with increasing myelin content, from 0.5kPa at a myelin content of 63-2.5kPa at 92%.
MeSH term(s)	Animals ; Biomechanical Phenomena ; Brain/cytology ; Brain/physiology ; Cattle ; Myelin Sheath/metabolism ; White Matter/physiology
Language	English
Publishing date	2016--15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173841-5
ISSN	1878-7568 ; 1742-7061
ISSN (online)	1878-7568
ISSN	1742-7061
DOI	10.1016/j.actbio.2016.07.040
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