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Scientific Reports Jul 2023This paper deals with the mathematical modeling of bacterial co-aggregation and its numerical implementation in a FEM framework. Since the concept of co-aggregation...
This paper deals with the mathematical modeling of bacterial co-aggregation and its numerical implementation in a FEM framework. Since the concept of co-aggregation refers to the physical binding between cells of different microbial species, a system composed of two species is considered in the modeling framework. The extension of the model to an arbitrary number of species is straightforward. In addition to two-species (multi-species growth) dynamics, the transport of a nutritional substance and the extent of co-aggregation are introduced into the model as the third and fourth primary variables. A phase-field modeling approach is employed to describe the co-aggregation between the two species. The mathematical model is three-dimensional and fully based on the continuum description of the problem without any need for discrete agents which are the key elements of the individual-based modeling approach. It is shown that the use of a phase-field-based model is equivalent to a particular form of classical diffusion-reaction systems. Unlike the so-called mixture models, the evolution of each component of the multi-species system is captured thanks to the inherent capability of phase-field modeling in treating systems consisting of distinct multi-phases. The details of numerical implementation in a FEM framework are also presented. Indeed, a new multi-field user element is developed and implemented in ANSYS for this multiphysics problem. Predictions of the model are compared with the experimental observations. By that, the versatility and applicability of the model and the numerical tool are well established.
Topics: Diffusion; Physical Examination
PubMed: 37481628
DOI: 10.1038/s41598-023-38806-2 -
Acta Biomaterialia Jul 2024Magnetic resonance elastography (MRE) and diffusion-weighted imaging (DWI) are complementary imaging techniques that detect disease based on viscoelasticity and water...
Magnetic resonance elastography (MRE) and diffusion-weighted imaging (DWI) are complementary imaging techniques that detect disease based on viscoelasticity and water mobility, respectively. However, the relationship between viscoelasticity and water diffusion is still poorly understood, hindering the clinical translation of combined DWI-MRE markers. We used DWI-MRE to study 129 biomaterial samples including native and cross-linked collagen, glycosaminoglycans (GAGs) with different sulfation levels, and decellularized specimens of pancreas and liver, all with different proportions of solid tissue, or solid fractions. We developed a theoretical framework of the relationship between mechanical loss and tissue-water mobility based on two parameters, solid and fluid viscosity. These parameters revealed distinct DWI-MRE property clusters characterizing weak, moderate, and strong water-network interactions. Sparse networks interacting weakly with water, such as collagen or diluted decellularized tissue, resulted in marginal changes in water diffusion over increasing solid viscosity. In contrast, dense networks with larger solid fractions exhibited both free and hindered water diffusion depending on the polarity of the solid components. For example, polar and highly sulfated GAGs as well as native soft tissues hindered water diffusion despite relatively low solid viscosity. Our results suggest that two fundamental properties of tissue networks, solid fraction and network polarity, critically influence solid and fluid viscosity in biological tissues. Since clinical DWI and MRE are sensitive to these viscosity parameters, the framework we present here can be used to detect tissue remodeling and architectural changes in the setting of diagnostic imaging. STATEMENT OF SIGNIFICANCE: The viscoelastic properties of biological tissues provide a wealth of information on the vital state of cells and host matrix. Combined measurement of viscoelasticity and water diffusion by medical imaging is sensitive to tissue microarchitecture. However, the relationship between viscoelasticity and water diffusion is still poorly understood, hindering full exploitation of these properties as a combined clinical biomarker. Therefore, we analyzed the parameter space accessible by diffusion-weighted imaging (DWI) and magnetic resonance elastography (MRE) and developed a theoretical framework for the relationship between water mobility and mechanical parameters in biomaterials. Our theory of solid material properties related to particle motion can be translated to clinical radiology using clinically established MRE and DWI.
Topics: Viscosity; Water; Diffusion; Animals; Elasticity; Elasticity Imaging Techniques; Humans; Diffusion Magnetic Resonance Imaging; Collagen; Glycosaminoglycans; Liver
PubMed: 38729549
DOI: 10.1016/j.actbio.2024.05.007 -
Journal of Environmental Management Nov 2023Urbanization and land use change are leading causes of declines in pollinator abundance and diversity. However, researchers in different regions of the world have found...
Urbanization and land use change are leading causes of declines in pollinator abundance and diversity. However, researchers in different regions of the world have found that some pollinators can thrive in urban landscapes, depending on land use practices, environmental conditions, and species traits. Residential landscapes constitute a significant portion of urban green space and thus, residents' adoption of landscape practices to promote pollinators can play a central role in addressing the global pollinator challenge. Yet, although residents' willingness and intention appear strong, adoption of pollinator-friendly gardening remains low. The present study - guided by the Diffusion of Innovations theory - aimed to build empirical understanding by surveying 1598 [State] residents on their experiences and perceptions related to pollinator-friendly gardening to determine the most salient barriers and opportunities to engagement. Key findings suggest making the practice more widely observable and reducing perceived complexity in learning to do the practice are critical to promoting adoption. This demonstrates, in practical terms, that: (1) targeted efforts to build residents' actionable knowledge about pollinator-friendly gardening may significantly reduce uncertainty and boost the likelihood of adoption; and (2) examples of active pollinator gardens need to be more widely showcased and popularized (e.g., through experiential or virtual demonstrations). We also found most residents living in homeowner associations (HOAs) believed HOA policies on pollinator-friendly gardening were restrictive or the residents were unsure whether they are allowed to practice pollinator-friendly gardening. Given these perceptions strongly associated with residents' low intent to engage in pollinator-friendly gardening, a major opportunity exists to diffuse the practice and increase adoption by working with HOAs and community leaders to become promoters of - rather than barriers to - pollinator-friendly gardening.
Topics: Gardening; Diffusion; Gardens; Intention; Knowledge
PubMed: 37708642
DOI: 10.1016/j.jenvman.2023.118877 -
Brain Communications 2023White matter is often severely affected after human ischaemic stroke. While animal studies have suggested that various factors may contribute to white matter structural...
White matter is often severely affected after human ischaemic stroke. While animal studies have suggested that various factors may contribute to white matter structural damage after ischaemic stroke, the characterization of damaging processes to the affected hemisphere after human stroke remains poorly understood. Thus, the present study aims to thoroughly describe the longitudinal pattern of evolution of diffusion magnetic resonance imaging metrics in different parts of the ipsilesional white matter after stroke. We acquired diffusion and anatomical images in 17 patients who had suffered from a single left hemisphere ischaemic stroke, at 24-72 h, 8-14 days and 6 months post-stroke. For each patient, we created three regions of interest: (i) the white matter lesion; (ii) the perilesional white matter; and (iii) the remaining white matter of the left hemisphere. We extracted diffusion metrics (fractional anisotropy, mean, axial and radial diffusivities) for each region and conducted two-way repeated measures ANOVAs with stage post-stroke (acute, subacute and chronic) × regions of interest (white matter lesion, perilesional white matter and remaining white matter). Fractional anisotropy values stayed consistent across time-points, with significantly lower values in the white matter lesion compared to the perilesional white matter and remaining white matter tissue. Fractional anisotropy values of the perilesional white matter were also significantly lower than that of the remaining white matter. Mean, axial and radial diffusivities in the white matter lesion were all decreased in the acute stage compared to perilesional white matter and remaining white matter, but significantly increased in both the subacute and chronic stages. Significant increases in mean and radial diffusivities in the perilesional white matter were seen in the later stages of stroke. Our findings suggest that various physiological processes are at play in the acute, subacute and chronic stages following ischaemic stroke, with the infarct territory and perilesional white matter affected by ischaemia at different rates and to different extents throughout the stroke recovery stages. The examination of multiple diffusivity metrics may inform us about the mechanisms occurring at different time-points, i.e. focal swelling, axonal damage or myelin loss.
PubMed: 38075947
DOI: 10.1093/braincomms/fcad313 -
Journal of Mathematical Biology Nov 2023Autoimmune diseases, such as Multiple Sclerosis, are often modelled through the dynamics of T-cell interactions. However, the spatial aspect of such diseases, and how...
Autoimmune diseases, such as Multiple Sclerosis, are often modelled through the dynamics of T-cell interactions. However, the spatial aspect of such diseases, and how dynamics may result in spatially heterogeneous outcomes, is often overlooked. We consider the effects of diffusion and chemotaxis on T-cell regulatory dynamics using a three-species model of effector and regulator T-cell populations, along with a chemical signalling agent. While diffusion alone cannot lead to instability and spatial patterning, the inclusion of chemotaxis can result in multiple forms of instability that produce highly complicated spatiotemporal behaviour. The parameter regimes in which different instabilities occur are determined through linear stability analysis and the full dynamics is explored through numerical simulation.
Topics: Chemotaxis; Models, Biological; T-Lymphocytes; Signal Transduction; Cell Communication; Computer Simulation; Diffusion
PubMed: 37947884
DOI: 10.1007/s00285-023-02017-0 -
Environmental Science and Pollution... Dec 2023Rapid degradation of quality and quantity of the available limited fresh water reserves has forced nations around the globe to search for alternate fresh water sources.... (Review)
Review
Rapid degradation of quality and quantity of the available limited fresh water reserves has forced nations around the globe to search for alternate fresh water sources. This has led to the development of various desalination technologies to generate potable water from abundantly available sea and brackish water. Desalination sector has undergone various upgradations to meet the rising fresh water demand in a sustainable way. One such upgradation is the utilization of solar energy as an energy source. High cost and associated environmental impacts with large-scale desalination systems have shifted the focus of researchers towards research and development of various small-scale efficient solar stills for cheap potable water production in rural, remote, arid, and coastal locations. In this review article, various configurations of a non-conventional solar still, namely inverted solar still, have been reviewed extensively by highlighting its classifications, design aspects, working principle, features, and economics. Moreover, the role of inverted solar still's evaporating and condensing surface characteristics and thermal properties on its distillate productivity has also been discussed. Inverted absorber multi-basin solar still and inverted multi-effect diffusion solar still configurations are highly productive. Economics of inverted solar still is better than other conventional solar still configurations and conventional reverse osmosis plant of few m/day capacity. This review article will facilitate researchers to select appropriate inverted solar still configuration for further performance improvement and commercialization. The scope for future research works on inverted solar still has also been listed.
Topics: Water; Drinking Water; Fresh Water; Solar Energy; Diffusion; Energy-Generating Resources; Water Purification
PubMed: 37964147
DOI: 10.1007/s11356-023-30760-w -
Proceedings of the National Academy of... Sep 2023Metabolic scaling theory (MST) provides an understanding of scaling in organismal morphology. Empirical data on the apparently universal pattern of tip-to-base conduit...
Metabolic scaling theory (MST) provides an understanding of scaling in organismal morphology. Empirical data on the apparently universal pattern of tip-to-base conduit widening across vascular plants motivate a set of generalized MST (gMST) relationships allowing for variable rates of conduit coalescence and taper and a transition between transport and diffusive domains. Our model, with coalescence limited to the distalmost part of the conductive system, reconciles previous MST-based models and extends their applicability to the entire plant. We derive an inverse relationship between stem volume taper and conduit widening, which implies that plant morphology is dictated by vascular optimality and not the assumption of constant sapwood area across all branching levels, contradicting Leonardo's rule. Thus, energy efficiency controls conduit coalescence rate, lowering the carbon cost needed to sustain the vascular network. Our model shows that as a plant grows taller, it must increase conduit widening and coalescence, which may make it more vulnerable to drought. We calculated how our gMST model implies a lower carbon cost to sustain a similar network compared to previous MST-based models. We also show that gMST predicts the cross-sectional area of vessels and their frequency along the relative length better than previous MST models for a range of plant types. We encourage further research obtaining data that would allow testing other gMST predictions that remain unconfirmed empirically, such as conduit coalescence rate in stems. The premise of energy efficiency can potentially become instrumental to our understanding of plant carbon allocation.
Topics: Tracheophyta; Carbon; Cardiac Conduction System Disease; Diffusion; Droughts
PubMed: 37722036
DOI: 10.1073/pnas.2215047120 -
Journal of the Mechanical Behavior of... Jan 2024Hydrogels are a promising class of material in biomedical and industrial applications, where both the mechanical and diffusion properties play an important role. The...
Hydrogels are a promising class of material in biomedical and industrial applications, where both the mechanical and diffusion properties play an important role. The wide range of polymers that can be used and the different production methods allows these properties to be specifically tuned to a high degree for their application. Producing tough hydrogels with high stiffness has been a long-standing challenge that has recently been addressed by mineralisation methods. Those methods modify the hydrogel into one with a supporting mineral microstructure that is highly heterogeneous. This work investigates methods to determine the macroscopic diffusion behaviour of heterogeneous gels by a homogenisation method implemented in a finite element framework. This is applied to two recently developed materials by calcifying poly-dimethyl-acrylamide (PDMA) and polyacrylamide hydrogels (PAAm). The former has porous, spherical inclusions obstructing diffusion, while the latter has spherical pores enabling it. For both gels the unobstructed volume can be used as the primary parameter to tune the diffusivity. In PDMA the porosity of the obstructions is shown by multiscale analysis to give a strong, non-linear dependence of the diffusivity on the solute molecule radius. The framework is extended to other materials and comparisons are made to experimental works from the literature.
Topics: Hydrogels; Polymers; Calcification, Physiologic; Porosity; Diffusion
PubMed: 37988844
DOI: 10.1016/j.jmbbm.2023.106244 -
Development (Cambridge, England) Nov 2023Plant external surfaces are often covered by barriers that control the exchange of molecules, protect from pathogens and offer mechanical integrity. A key question is...
Plant external surfaces are often covered by barriers that control the exchange of molecules, protect from pathogens and offer mechanical integrity. A key question is when and how such surface barriers are generated. Post-embryonic surfaces have well-studied barriers, including the cuticle, and it has been previously shown that the late Arabidopsis thaliana embryo is protected by an endosperm-derived sheath deposited onto a primordial cuticle. Here, we show that both cuticle and sheath are preceded by another structure during the earliest stages of embryogenesis. This structure, which we named the embryonic envelope, is tightly wrapped around the embryonic surface but can be physically detached by cell wall digestion. We show that this structure is composed primarily of extensin and arabinogalactan O-glycoproteins and lipids, which appear to form a dense and elastic crosslinked embryonic envelope. The envelope forms in cuticle-deficient mutants and in a mutant that lacks endosperm. This embryo-derived envelope is therefore distinct from previously described cuticle and sheath structures. We propose that it acts as an expandable diffusion barrier, as well as a means to mechanically confine the embryo to maintain its tensegrity during early embryogenesis.
Topics: Arabidopsis; Arabidopsis Proteins; Seeds; Endosperm; Diffusion; Gene Expression Regulation, Plant
PubMed: 37869985
DOI: 10.1242/dev.201943 -
Magnetic Resonance in Medicine Jun 2024Dynamic (2D) MRS is a collection of techniques where acquisitions of spectra are repeated under varying experimental or physiological conditions. Dynamic MRS comprises a...
PURPOSE
Dynamic (2D) MRS is a collection of techniques where acquisitions of spectra are repeated under varying experimental or physiological conditions. Dynamic MRS comprises a rich set of contrasts, including diffusion-weighted, relaxation-weighted, functional, edited, or hyperpolarized spectroscopy, leading to quantitative insights into multiple physiological or microstructural processes. Conventional approaches to dynamic MRS analysis ignore the shared information between spectra, and instead proceed by independently fitting noisy individual spectra before modeling temporal changes in the parameters. Here, we propose a universal dynamic MRS toolbox which allows simultaneous fitting of dynamic spectra of arbitrary type.
METHODS
A simple user-interface allows information to be shared and precisely modeled across spectra to make inferences on both spectral and dynamic processes. We demonstrate and thoroughly evaluate our approach in three types of dynamic MRS techniques. Simulations of functional and edited MRS are used to demonstrate the advantages of dynamic fitting.
RESULTS
Analysis of synthetic functional H-MRS data shows a marked decrease in parameter uncertainty as predicted by prior work. Analysis with our tool replicates the results of two previously published studies using the original in vivo functional and diffusion-weighted data. Finally, joint spectral fitting with diffusion orientation models is demonstrated in synthetic data.
CONCLUSION
A toolbox for generalized and universal fitting of dynamic, interrelated MR spectra has been released and validated. The toolbox is shared as a fully open-source software with comprehensive documentation, example data, and tutorials.
Topics: Magnetic Resonance Spectroscopy; Software; Contrast Media; Diffusion; Uncertainty
PubMed: 38265152
DOI: 10.1002/mrm.30001