Mathematical models and numerical simulation of mechanochemical pattern formation in biological tissues

Mechanical and chemical pattern formation in the development of biological tissue is a fundamental and fascinating process of self-complexation and self-organization. Yet, the understanding of the underlying mechanisms and their mathematical description still lacks in many interesting cases such as embryogenesis. In this thesis, we combine recent experimental and theoretical insights and numerically investigate the capacity of mechano-chemical processes to spontaneously generate patterns in biological tissue. Firstly, we develop and numerically analyze a prototypical system of partial differential equations (PDEs) leading to mechanochemical pattern formation in evolving tissues. Based on recent experimental data, we propose a novel coupling by tensor invariants describing stretch, stress or strain of tissue mechanics on the production of signaling molecules (morphogens). In turn, morphogen leads to piecewise-defined active deformations of individual biological cells. The presented approach is flexible and applied to two prominent examples of evolving tissue: We show how these simple interaction rules (“feedback loops”) lead to spontaneous, robust mechanochemical patterns in the applications to embryogenesis and to symmetry breaking in the sweet water polyp Hydra. Our results reveal that the full 3D model geometry is essential to obtain realistic results such as gastrulation events. Also, we highlight predictive numerical experiments that assess the sensitivity of biological tissue with regard to mechanical stimuli, namely to micropipette aspiration. These numerical experiments allow for a cross-validation with experimental observations. Besides, we apply our modeling approach to growing tips in colonial hydroids and investigate the role of rotational and shearing active deformations by comparison to experimental data. Secondly, we develop an efficient, numerical method to reliably solve these strongly coupled, prototypical systems of PDEs that model mechanochemical long-term problems. We employ state-of-the-art finite element methods, parallel geometric multigrid solvers and present a simple, local mesh refinement strategy to obtain an efficient solution approach. Parallel solvers are essential to deal with the huge problem size in 3D and were modified to keep track of biological cells. Further, we propose a stabilization of the structural equation to deal with the strongly coupled system of equations and the challenges of the different timescales of growth (days) and nonlinear elasticity (seconds). Also, this addresses the instabilities which result form the description of homogeneous Neumann values on the entire boundary that is necessary since the locations of patterns is a priori unknown

Sweet cherry flesh cells burst in non-random clusters along minor veins

Main conclusion: Sweet cherry flesh cells burst when exposed to water but they do so in clusters indicating heterogeneity with respect to osmotic concentration, which depends on proximity to a minor vein. Abstract: Water plays a key role in cracking in sweet cherry fruit. Magnetic resonance imaging has previously indicated preferential partitioning of water along veins. A more negative osmotic potential along veins seems the likely explanation. Here we establish if cell bursting in mature sweet cherry fruit is also associated with the veins. Cell bursting was identified by a novel light microscope technique involving exposure of a cut fruit surface to water or to sucrose solutions. Upon exposure to water there was no bursting of skin cells but for cells of the flesh (mesocarp) bursting increased with time. When the cut surface was exposed to sucrose solutions of decreasing osmotic concentrations (increasing water potentials) the incidence of cell bursting increased from hypertonic (no bursting), to isotonic, to hypotonic. Cell bursting in the outer mesocarp occurred primarily in the vicinity of minor veins that in the inner mesocarp was primarily between radial veins. The median distance between a minor vein and a bursting cell (mean diameter 0.129 mm) was about 0.318 mm that between a radial vein and a bursting cell was about 0.497 mm. In contrast, the distance between adjacent minor veins averaged 2.57 mm, that between adjacent radial veins averaged 0.83 mm. Cell bursting tends to occur in clusters. Mapping of cell bursting indicates (1) that a seemingly uniform population of mesocarp cells actually represents a heterogeneous population with regard to their cell osmotic potentials and (2) cell bursting afflicts clusters of neighbouring cells in the vicinities of minor veins

Exploring Online Depression Forums via Text Mining: A Comparison of Reddit and a Curated Online Forum

We present a study employing various techniques of text mining to explore and compare two different online forums focusing on depression: (1) the subreddit r/depression (over 60 million tokens), a large, open social media platform and (2) Beyond Blue (almost 5 million tokens), a professionally curated and moderated depression forum from Australia. We are interested in how the language and the content on these platforms differ from each other. We scrape both forums for a specific period. Next to general methods of computational text analysis, we focus on sentiment analysis, topic modeling and the distribution of word categories to analyze these forums. Our results indicate that Beyond Blue is generally more positive and that the users are more supportive to each other. Topic modeling shows that Beyond Blue's users talk more about adult topics like finance and work while topics shaped by school or college terms are more prevalent on r/depression. Based on our findings we hypothesize that the professional curation and moderation of a depression forum is beneficial for the discussion in it

Beyond Turing: mechanochemical pattern formation in biological tissues

Background: During embryogenesis, chemical (morphogen) and mechanical patterns develop within tissues in a self-organized way. More than 60 years ago, Turing proposed his famous reaction-diffusion model for such processes, assuming chemical interactions as the main driving force in tissue patterning. However, experimental identification of corresponding molecular candidates is still incomplete. Recent results suggest that beside morphogens, also tissue mechanics play a significant role in these patterning processes. Results: Combining continuous finite strain with discrete cellular tissue models, we present and numerically investigate mechanochemical processes, in which morphogen dynamics and tissue mechanics are coupled by feedback loops. We consider three different mechanical cues involved in such feedbacks: strain, stress, and compression. Based on experimental results, for each case, we present a feedback loop spontaneously creating robust mechanochemical patterns. In contrast to Turing-type models, simple mechanochemical interaction terms are sufficient to create de novo patterns. Conclusions: Our results emphasize mechanochemical processes as possible candidates controlling different steps of embryogenesis. To motivate further experimental research discovering related mechanisms in living tissues, we also present predictive in silicio experiments. Reviewers: Reviewer 1 - Marek Kimmel; Reviewer 2 - Konstantin Doubrovinski (nominated by Ned Wingreen); Reviewer 3 - Jun Allard (nominated by William Hlavacek)

Best Available Techniques (BAT) Reference Document for Large Combustion Plants. Industrial Emissions Directive 2010/75/EU (Integrated Pollution Prevention and Control)

The BAT Reference Document (BREF) for Large Combustion Plants is part of a series of documents presenting the results of an exchange of information between the EU Member States, the industries concerned, non-governmental organisations promoting environmental protection, and the Commission, to draw up, review, and -where necessary- update BAT reference documents as required by Article 13(1) of Directive 2010/75/EU on Industrial Emissions. This document is published by the European Commission pursuant to Article 13(6) of the Directive. This BREF for Large Combustion Plants concerns the following activities specified in Annex I to Directive 2010/75/EU: - 1.1: Combustion of fuels in installations with a total rated thermal input of 50 MW or more, only when this activity takes place in combustion plants with a total rated thermal input of 50 MW or more. - 1.4: Gasification of coal or other fuels in installations with a total rated thermal input of 20 MW or more, only when this activity is directly associated to a combustion plant. - 5.2: Disposal or recovery of waste in waste co-incineration plants for non-hazardous waste with a capacity exceeding 3 tonnes per hour or for hazardous waste with a capacity exceeding 10 tonnes per day, only when this activity takes place in combustion plants covered under 1.1 above. In particular, this document covers upstream and downstream activities directly associated with the aforementioned activities including the emission prevention and control techniques applied. The fuels considered in this document are any solid, liquid and/or gaseous combustible material including: - solid fuels (e.g. coal, lignite, peat); - biomass (as defined in Article 3(31) of Directive 2010/75/EU); - liquid fuels (e.g. heavy fuel oil and gas oil); - gaseous fuels (e.g. natural gas, hydrogen-containing gas and syngas); - industry-specific fuels (e.g. by-products from the chemical and iron and steel industries); - waste except mixed municipal waste as defined in Article 3(39) and except other waste listed in Article 42(2)(a)(ii) and (iii) of Directive 2010/75/EU. Important issues for the implementation of Directive 2010/75/EU in the Large Combustion Plants sector are the emissions to air of nitrogen oxides, sulphur dioxide, hydrogen chloride and fluoride, organic compounds, dust, and metals including mercury; emissions to water resulting especially from the use of wet abatement techniques for the removal of sulphur dioxide from the flue gases; resource efficiency and especially energy efficiency. This BREF contains 12 Chapters. Chapters 1 and 2 provide general information on the Large Combustion Plants industrial sector and on the industrial processes used within this sector. Chapter 3 provides data and general information concerning the environmental performance of installations within the sector in terms of water consumption, the generation of waste and general techniques used within this sector. It also describes in more detail the general techniques to prevent or, where this is not practicable, to reduce the environmental impact of installations in this sector that were considered in determining the BAT. Chapters 4 to 9 provide the following information given below on specific combustion processes (gasification, combustion of solid fuel, combustion of liquid fuel, combustion of gaseous fuel, multi-fuel combustion and waste co-incineration). Chapter 10 presents the BAT conclusions as defined in Article 3(12) of the Directive. Chapter 11 presents information on 'emerging techniques' as defined in Article 3(14) of the Directive. Concluding remarks and recommendations for future work are presented in Chapter 12.JRC.B.5-Circular Economy and Industrial Leadershi

Impact of the contacting scheme on I-V measurements of metallization-free silicon heterojunction solar cells

I-V measurements are sensitive to the number and positioning of current and voltage sensing contacts. For busbarless solar cells, measurement setups have been developed using current collection wires and separate voltage sense contacts. Placing the latter at a defined position enables a grid resistance neglecting measurement and thus I-V characteristics independent from the contacting system. This technique has been developed for solar cells having a finger grid and good conductivity in the direction of the fingers. The optimal position of the sense contact in case of finger-free silicon heterojunction solar cells has not yet been studied. Here, the lateral charge carrier transport occurs in a transparent conductive oxide layer resulting in a higher lateral resistance. We perform finite difference method simulations of HJT solar cells without front metallization to investigate the impact of high lateral resistances on the I-V measurement of solar cells. We show the high sensitivity on the number of used wires for contacting as well as the position of the sense contact for the voltage measurement. Using the simulations, we are able to explain the high difference of up to 7.5% in fill factor measurements of metal free solar cells with varying TCO sheet resistances between two measurement systems using different contacting setups. We propose a method to compensate for the contacting system to achieve a grid-resistance neglecting measurement with both systems allowing a reduction of the FF difference to below 1.5%

Development of a GEM-TPC prototype

The use of GEM foils for the amplification stage of a TPC instead of a con- ventional MWPC allows one to bypass the necessity of gating, as the backdrift is suppressed thanks to the asymmetric field configuration. This way, a novel continuously running TPC, which represents one option for the PANDA central tracker, can be realized. A medium sized prototype with a diameter of 300 mm and a length of 600 mm will be tested inside the FOPI spectrometer at GSI using a carbon or lithium beam at intermediate energies (E = 1-3AGeV). This detector test under realistic experimental conditions should allow us to verify the spatial resolution for single tracks and the reconstruction capability for displaced vertexes. A series of physics measurement implying pion beams is scheduled with the FOPI spectrometer together with the GEM-TPC as well.Comment: 5 pages, 4 figures, Proceedings for 11th ICATTP conference in como (italy