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| 15. |
- Ahooghalandari, Parvin, et al.
(författare)
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Mutations in Arg143 and Lys192 of the Human Mast Cell Chymase Markedly Affect the Activity of Five Potent Human Chymase Inhibitors
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:6, s. e65988-
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Tidskriftsartikel (refereegranskat)abstract
- Chymotrypsin-like serine proteases are found in high abundance in mast cell granules. By site-directed mutatgenesis, we have previously shown that basic amino acids in positions 143 and 192 (Arg and Lys respectively) of the human mast cell chymase are responsible for an acidic amino acid residue preference in the P2' position of substrates. In order to study the influence of these two residues in determining the specificity of chymase inhibitors, we have synthesized five different potent inhibitors of the human chymase. The inhibitory effects of these compounds were tested against the wild-type enzyme, against two single mutants Arg143Gln and Lys192Met and against a double mutant, Arg143Gln+Lys192Met. We observed a markedly reduced activity of all five inhibitors with the double mutant, indicating that these two basic residues are involved in conferring the specificity of these inhibitors. The single mutants showed an intermediate phenotype, with the strongest effect on the inhibitor by the mutation in Lys192. The Lys192 and the double mutations also affected the rate of cleavage of angiotensin I but did not seem to affect the specificity in the cleavage of the Tyr(4)-Ile(5) bond. A more detailed knowledge about which amino acids that confer the specificity of an enzyme can prove to be of major importance for development of highly specific inhibitors for the human chymase and other medically important enzymes.
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| 16. |
- Baqué, Mickael, et al.
(författare)
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Biosignature stability in space enables their use for life detection on Mars
- 2022
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Ingår i: Science Advances. - : NLM (Medline). - 2375-2548. ; 8:36
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Tidskriftsartikel (refereegranskat)abstract
- Two rover missions to Mars aim to detect biomolecules as a sign of extinct or extant life with, among other instruments, Raman spectrometers. However, there are many unknowns about the stability of Raman-detectable biomolecules in the martian environment, clouding the interpretation of the results. To quantify Raman-detectable biomolecule stability, we exposed seven biomolecules for 469 days to a simulated martian environment outside the International Space Station. Ultraviolet radiation (UVR) strongly changed the Raman spectra signals, but only minor change was observed when samples were shielded from UVR. These findings provide support for Mars mission operations searching for biosignatures in the subsurface. This experiment demonstrates the detectability of biomolecules by Raman spectroscopy in Mars regolith analogs after space exposure and lays the groundwork for a consolidated space-proven database of spectroscopy biosignatures in targeted environments.
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| 17. |
- Blanco, Nicolas E., et al.
(författare)
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Expression of the Minor Isoform Pea Ferredoxin in Tobacco Alters Photosynthetic Electron Partitioning and Enhances Cyclic Electron Flow
- 2013
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 161:2, s. 866-879
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Tidskriftsartikel (refereegranskat)abstract
- Ferredoxins (Fds) are ferrosulfoproteins that function as low-potential electron carriers in plants. The Fd family is composed of several isoforms that share high sequence homology but differ in functional characteristics. In leaves, at least two isoforms conduct linear and cyclic photosynthetic electron transport around photosystem I, and mounting evidence suggests the existence of at least partial division of duties between these isoforms. To evaluate the contribution of different kinds of Fds to the control of electron fluxes along the photosynthetic electron transport chain, we overexpressed a minor pea (Pisum sativum) Fd isoform (PsFd1) in tobacco (Nicotiana tabacum) plants. The transplastomic OeFd1 plants exhibited variegated leaves and retarded growth and developmental rates. Photosynthetic studies of these plants indicated a reduction in carbon dioxide assimilation rates, photosystem II photochemistry, and linear electron flow. However, the plants showed an increase in nonphotochemical quenching, better control of excitation pressure at photosystem II, and no evidence of photoinhibition, implying a better dynamic regulation to remove excess energy from the photosynthetic electron transport chain. Finally, analysis of P700 redox status during illumination confirmed that the minor pea Fd isoform promotes enhanced cyclic flow around photosystem I. The two novel features of this work are: (1) that Fd levels achieved in transplastomic plants promote an alternative electron partitioning even under greenhouse light growth conditions, a situation that is exacerbated at higher light intensity measurements; and (2) that an alternative, minor Fd isoform has been overexpressed in plants, giving new evidence of labor division among Fd isoforms.
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| 19. |
- Brandi, Maya, et al.
(författare)
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Multiscale modeling through MUSIC multi-simulation : Modeling a dendritic spine using MOOSE and NeuroRD
- 2011
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Ingår i: Front. Neuroinform. Conference Abstract. - : Frontiers Media SA.
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Konferensbidrag (refereegranskat)abstract
- The nervous system encompasses structure and phenomena at different spatial and temporal scales from molecule to behavior. In addition, different scales are described by different physical and mathematical formalisms. The dynamics of second messenger pathways can be formulated as stochastic reaction-diffusion systems [1] while the electrical dynamics of the neuronal membrane is often described by compartment models and the Hodgkin-Huxley formalism. In neuroscience, there is an increasing need and interest to study multi-scale phenomena where multiple scales and physical formalisms are covered by a single model. While there exists simulators/frameworks, such as GENESIS and MOOSE [3], which span such scales (kinetikit/HH-models), most software applications are specialized for a given domain. Here, we report about initial steps towards a framework for multi-scale modeling which builds on the concept of multi-simulations [2]. We aim to provide a standard API and communication framework allowing parallel simulators targeted at different scales and/or different physics to communicate on-line in a cluster environment. Specifically, we show prototype work on simulating the effect on receptor induced cascades on membrane excitability. Electrical properties of a compartment model is simulated in MOOSE, while receptor induced cascades are simulated in NeuroRD [4,7] . In a prototype system, the two simulators are connected using PyMOOSE [5] and JPype [6]. The two models with their different physical properties (membrane currents in MOOSE, molecular biophysics in NeuroRD), are joined into a single model system. We demonstrate the interaction of the numerical solvers of two simulators (MOOSE, NeuroRD) targeted at different spatiotemporal scales and different physics while solving a multi-scale problem. We analyze some of the problems that may arise in multi-scale multi-simulations and present requirements for a generic API for parallel solvers. This work represents initial steps towards a flexible modular framework for simulation of large-scale multi-scale multi-physics problems in neuroscience. References 1. Blackwell KT: An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines. J Neurosci Meth 2006, 157: 142-153. 2. Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Hellgren Kotaleski J, Ekeberg Ö: Run-Time Interoperability Between Neural Network Simulators Based on the MUSIC Framework. Neurinform 2010, 8: 43-60. 3. Dudani N, Ray S, George S, Bhalla US: Multiscale modeling and interoperability in MOOSE. Neuroscience 2009, 10(Suppl 1): 54. 4. Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blacwell KT: The Role of Type 4 Phosphdiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations.
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| 20. |
- Brocke, Ekaterina, et al.
(författare)
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Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations
- 2016
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Ingår i: Frontiers in Computational Neuroscience. - : Frontiers Media SA. - 1662-5188. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. First, the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. Then, the components can be defined by different mathematical formalisms. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, in neuroscience, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components comprising a multiscale test problem in neuroscience. We introduce an efficient coupling method based on the second-order backward differentiation formula (BDF2) numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000). The method shows a significant advantage over conventional fixed step size solvers used in neuroscience for similar problems. We explore different coupling strategies that define the organization of computations between system components. We study the importance of an appropriate approximation of exchanged variables during the simulation. The analysis shows a substantial impact of these aspects on the solution accuracy in the application to our multiscale neuroscientific test problem. We believe that the ideas presented in the paper may essentially contribute to the development of a robust and efficient framework for multiscale brain modeling and simulations in neuroscience.
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| 21. |
- Brocke, Ekaterina, et al.
(författare)
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Multirate method for co-simulation of electrical-chemical systems in multiscale modeling
- 2017
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Ingår i: Journal of Computational Neuroscience. - : Springer-Verlag New York. - 0929-5313 .- 1573-6873. ; 42:3, s. 245-256
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Tidskriftsartikel (refereegranskat)abstract
- Multiscale modeling by means of co-simulation is a powerful tool to address many vital questions in neuroscience. It can for example be applied in the study of the process of learning and memory formation in the brain. At the same time the co-simulation technique makes it possible to take advantage of interoperability between existing tools and multi-physics models as well as distributed computing. However, the theoretical basis for multiscale modeling is not sufficiently understood. There is, for example, a need of efficient and accurate numerical methods for time integration. When time constants of model components are different by several orders of magnitude, individual dynamics and mathematical definitions of each component all together impose stability, accuracy and efficiency challenges for the time integrator. Following our numerical investigations in Brocke et al. (Frontiers in Computational Neuroscience, 10, 97, 2016), we present a new multirate algorithm that allows us to handle each component of a large system with a step size appropriate to its time scale. We take care of error estimates in a recursive manner allowing individual components to follow their discretization time course while keeping numerical error within acceptable bounds. The method is developed with an ultimate goal of minimizing the communication between the components. Thus it is especially suitable for co-simulations. Our preliminary results support our confidence that the multirate approach can be used in the class of problems we are interested in. We show that the dynamics ofa communication signal as well as an appropriate choice of the discretization order between system components may have a significant impact on the accuracy of the coupled simulation. Although, the ideas presented in the paper have only been tested on a single model, it is likely that they can be applied to other problems without loss of generality. We believe that this work may significantly contribute to the establishment of a firm theoretical basis and to the development of an efficient computational framework for multiscale modeling and simulations.
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| 22. |
- Chaudhry, Qasim Ali
(författare)
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Computational Modeling of Reaction and Diffusion Processes in Mammalian Cell
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- PAHs are the reactive toxic chemical compounds which are present as environmental pollutants. These reactive compounds not only diffuse through the membranes of the cell but also partition into the membranes. They react with the DNA of the cell giving rise to toxicity and may cause cancer. To understand the cellular behavior of these foreign compounds, a mathematical model including the reaction-diffusion system and partitioning phenomenon has been developed. In order to reduce the complex structure of the cytoplasm due to the presence of many thin membranes, and to make the model less computationally expensive and numerically treatable, homogenization techniques have been used. The resulting complex system of PDEs generated from the model is implemented in Comsol Multiphysics. The numerical results obtained from the model show a nice agreement with the in vitro cell experimental results. Then the model was reduced to a system of ODEs, a compartment model (CM). The quantitative analysis of the results of the CM shows that it cannot fully capture the features of metabolic system considered in general. Thus the PDE model affords a more realistic representation. In order to see the influence of cell geometry in drug diffusion, the non-spherical axi-symmetric cell geometry is considered, where we showed that the cellular geometry plays an important role in diffusion through the membranes. For further reduction of complexity of the model, another simplified model was developed. In the simplified model, we used PDEs for the extracellular domain, cytoplasm and nucleus, whereas the plasma and nuclear membranes were taken away, and replaced by the membrane flux, using Fick's Law. We further extended the framework of our previously developed model by benchmarking against the results from four different cell lines. Global optimization techniques are used for the parameters describing the diffusion and reaction to fit the measured data. Numerical results were in good agreement with the in vitro results. For the further development of the model, the process of surface bound reactions were added, thus developing a new cell model. The effective equations were derived using iterative homogenization for this model. The numerical results of some of the species were qualitatively verified against the in vitro results found in literature.
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| 23. |
- Chaudhry, Qasim Ali, et al.
(författare)
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Influence of Biological Cell Geometry on Reaction and Diffusion Simulation
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Mathematical modeling of reaction-diffusion system in a biological cellis an important and difficult task, especially when the chemical compoundsare lipophilic. The difficulty level increases, when we take into account theheterogeneity of the cell, and the variation of cellular architecture. Mathematicalmodeling of reaction-diffusion systems in spherical cell geometryhas earlier been performed by us. In the present paper, we have workedwith non-spherical cell geometry, because the cellular geometry can play animportant role for drug diffusion in the cell. Homogenization techniques,which were earlier applied in the case of a spherical cell model, have beenused for the numerical treatment of the model. This technique considerablyreduces the complexity of the model. To further reduce the complexity ofthe model, a simplified model was also developed. The key idea of this simplifiedmodel has been advocated in Virtual Cell, where PDEs are used forthe extracellular domain, cytoplasm and nucleus, whereas the plasma andnuclear membranes have been taken away, and replaced by membrane flux,using Fick’s Law of diffusion. The numerical results of the non-sphericalcell model have been compared with the results of the spherical cell model,where the numerical results of spherical cell model have already been validatedagainst in vitro cell experimental results. From the numerical results,we conclude that the plasma and nuclear membranes can be protective reservoirsof significance. The numerical results of the simplified model werecompared against the numerical results of our detailed model, revealing theimportance of detailed modeling of membranes in our model.
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| 24. |
- Chaudhry, Qasim Ali, et al.
(författare)
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Mathematical Modeling of Reaction and Diffusion Systems in a Cell Including Surface Reactions on the Cytoplasmic Membranes
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Benzo[a]pyrene (BP) is a toxic polycyclic aromatic hydrocarbon (PAH) whichis found in our environment. These BPs are metabolized to benzo[a]pyrene diol(BPD) by enzymes bound to the cytoplasmic membranes e.g. members of thecytochrome P450 protein family and epoxide hydrolyses. BPDs are further metabolizedto two stereochemical variants of Benzo[a]pyrene diol expoxide (BPDE) bythe cytochrome P450 family of proteins. These are the two steps of metabolismcategorized as Phase I. In Phase II, BPDEs are further metabolized by soluble enzymesin the cytoplasm e.g. members of the glutathione transferase protein familyto GSH conjugates. BPDE can also diffuse into the cellular nucleus and reactwith DNA forming mutagenic DNA adducts. The formation of GSH conjugatesand DNA adducts, was earlier studied by us by developing a mathematical modeldescribing the intracellular reaction and diffusion of lipophilic PAHs taking intoaccount the partitioning phenomenon (Dreij K et al. PLoS One 6(8), 2011). In thispaper part of Phase I metabolism i.e formation of BPDE metabolites, will be addedto the model, thus enhancing the previous model. These cytochrome P450 reactionstake place on the intracellular membranes, and are modeled as a membranesurface reaction within the cytoplasm using the standard process of adsorption anddesorption. The effective equations are derived using iterative homogenization forthe numerical treatment of the cytoplasm including surface effects. The numericalresults of some of the species have been qualitatively verified against in vitroresults found in the literature.
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| 25. |
- Chaudhry, Qasim Ali, 1982-
(författare)
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Numerical Approximation of Reaction and Diffusion Systems in Complex Cell Geometry
- 2010
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The mathematical modelling of the reaction and diffusion mechanism of lipophilic toxic compounds in the mammalian cell is a challenging task because of its considerable complexity and variation in the architecture of the cell. The heterogeneity of the cell regarding the enzyme distribution participating in the bio-transformation, makes the modelling even more difficult. In order to reduce the complexity of the model, and to make it less computationally expensive and numerically treatable, Homogenization techniques have been used. The resulting complex system of Partial Differential Equations (PDEs), generated from the model in 2-dimensional axi-symmetric setting is implemented in Comsol Multiphysics. The numerical results obtained from the model show a nice agreement with the in vitro cell experimental results. The model can be extended to more complex reaction systems and also to 3-dimensional space. For the reduction of complexity and computational cost, we have implemented a model of mixed PDEs and Ordinary Differential Equations (ODEs). We call this model as Non-Standard Compartment Model. Then the model is further reduced to a system of ODEs only, which is a Standard Compartment Model. The numerical results of the PDE Model have been qualitatively verified by using the Compartment Modeling approach. The quantitative analysis of the results of the Compartment Model shows that it cannot fully capture the features of metabolic system considered in general. Hence we need a more sophisticated model using PDEs for our homogenized cell model.
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| 26. |
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| 27. |
- Chaudhry, Qasim Ali, 1982-, et al.
(författare)
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On the numerical approximation of drug diffusion in complex cell geometry
- 2009
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Ingår i: Proceedings of the 6th International Conference on Frontiers of Information Technology, FIT '09. - Abbottabad : ACM. - 9781605586427
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The mathematical modeling of a mammalian cell is a very tedious work due to its very complex geometry. Especially, taking into account the spatial distribution and the inclusion of lipophilic toxic compounds greatly increases its complexity. The nonhomogeneity and the different cellular architecture of the cell certainly affect the diffusion of these compounds. The complexity of the whole system can be reduced by a homogenization technique. To see the effect of these compounds on different cell architectures, we have implemented a mathematical model. The work has been done in 2-dimensional space. The simulation results have been qualitatively verified using compartmental modeling approach. This work can be extended with a more complex reaction-diffusion system and to 3-dimensional space as well. Copyright 2009 ACM.
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| 28. |
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| 29. |
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| 30. |
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| 31. |
- Chaudhry, Q. A., et al.
(författare)
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Surface reactions on the cytoplasmatic membranes - Mathematical modeling of reaction and diffusion systems in a cell
- 2014
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Ingår i: Journal of Computational and Applied Mathematics. - : Elsevier BV. - 0377-0427 .- 1879-1778. ; 262, s. 244-260
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Tidskriftsartikel (refereegranskat)abstract
- A human cell consists schematically of an outer cellular membrane, a cytoplasm containing a large number of organelles (mitochondria, endoplasmatic reticulum etc.), a nuclear membrane and finally the cellular nucleus containing DNA. The organelles create a complex and dense system of membranes or sub-domains throughout the cytoplasm. The mathematical description leads to a system of reaction-diffusion equations in a complex geometrical domain, dominated by thin membranous structures with similar physical and chemical properties. In a previous model, we considered only spatially distributed reaction and diffusion processes. However, from experiments it is known that membrane bound proteins play an important role in the metabolism of certain substances. In the present paper we develop a homogenization strategy which includes both volume and surface reactions. The homogenized system is a reaction-diffusion system in the cytoplasm which is coupled to the surrounding cell components by correspondingly modified transfer conditions. The approach is verified by application to a system modeling the cellular uptake and intracellular dynamics of carcinogenic polycyclic aromatic hydrocarbons.
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| 32. |
- Dreij, Kristian, et al.
(författare)
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A Method for Efficient Calculation of Diffusion and Reactions of Lipophilic Compounds in Complex Cell Geometry
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:8, s. e23128-
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Tidskriftsartikel (refereegranskat)abstract
- A general description of effects of toxic compounds in mammalian cells is facing several problems. Firstly, most toxic compounds are hydrophobic and partition phenomena strongly influence their behaviour. Secondly, cells display considerable heterogeneity regarding the presence, activity and distribution of enzymes participating in the metabolism of foreign compounds i.e. bioactivation/biotransformation. Thirdly, cellular architecture varies greatly. Taken together, complexity at several levels has to be addressed to arrive at efficient in silico modelling based on physicochemical properties, metabolic preferences and cell characteristics. In order to understand the cellular behaviour of toxic foreign compounds we have developed a mathematical model that addresses these issues. In order to make the system numerically treatable, methods motivated by homogenization techniques have been applied. These tools reduce the complexity of mathematical models of cell dynamics considerably thus allowing to solve efficiently the partial differential equations in the model numerically on a personal computer. Compared to a compartment model with well-stirred compartments, our model affords a more realistic representation. Numerical results concerning metabolism and chemical solvolysis of a polycyclic aromatic hydrocarbon carcinogen show good agreement with results from measurements in V79 cell culture. The model can easily be extended and refined to include more reactants, and/or more complex reaction chains, enzyme distribution etc, and is therefore suitable for modelling cellular metabolism involving membrane partitioning also at higher levels of complexity.
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| 33. |
- Dreij, Kristian, et al.
(författare)
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In silico Modeling of Intracellular Diffusion and Reaction of Benzo[a]pyrene Diol Epoxide
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Several studies has suggested that glutathione conjugation of polycyclicaromatic hydrocarbons (PAHs) catalyzed by glutathione transferases (GSTs)are important factors in protecting cells against toxicity and DNA damagederived from these compounds. To further characterize the intracellular dynamicsof PAH DEs and the role of GSTs in protection against DNA damage,we recently developed a PDE model using techniques for mathematicalhomogenization (Dreij K et al. PLoS One 6(8), 2011). In this study, wewanted to further develop our model by benchmarking against results fromfour V79 cell lines; control cells and cells overexpressing human GSTs A1-1, M1-1 and P1-1. We used an approach of global optimization of the parametersdescribing the diffusion and reaction of the ultimate carcinogenic PAHmetabolite benzo[a]pyrene diol epoxide to fit measured values from the fourV79 cell lines. Numerical results concerning the formation of glutathioneconjugates and hydrolysis were in good agreement with results from measurementsin V79 cell culture. Cellular results showed significant protectionby GST expression against formation of DNA adducts with more than 10-fold reduced levels compared to control cells. Results from the model usingglobally optimized parameters showed that the model cannot predict theprotective effects of GSTs. Extending the model to also include effects fromprotein interactions and GST localization showed the same discrepancy. Insummary, the results show that we have an incomplete understanding of theintracellular dynamics of the interaction between BPDE and GST that warrantsfurther investigation and development of the model.
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| 34. |
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| 35. |
- Hanke, Michael
(författare)
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A note on the consistent initialization for nonlinear index-2 differential-algebraic equations in Hessenberg form
- 2004
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In a previous paper, we developed a new algorithm for the consistent initialization of general index-2 differential-algebraic equations arising within the method of lines for solving partial differential equations. In the case of Hessenberg systems, the structural information allows for a lot of simplifications thus allowing for much larger systems to be solved. The crucial point consists of providing sparse projections by the use of sparse approximations to the inverse of the mass matrix. We obtain almost linear computational complexity with respect to the number of degrees of freedom.
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| 36. |
- Hanke, Michael, et al.
(författare)
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A reliable direct numerical treatment of differential–algebraic equations by overdetermined collocation : An operator approach
- 2021
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Ingår i: Journal of Computational and Applied Mathematics. - : Elsevier BV. - 0377-0427 .- 1879-1778. ; 387
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Tidskriftsartikel (refereegranskat)abstract
- Recently reported experiments and theoretical contributions concerning overdetermined polynomial collocation applied to higher-index differential–algebraic equations give rise to the conjecture that next to the existing derivative-array based methods there is further potential toward a reliable direct numerical treatment of DAEs. By analyzing first-order differential–algebraic operators and their special approximations in detail, we contribute to justify the overdetermined polynomial collocation applied to first-order higher-index differential–algebraic equations and fill the hitherto existing gap between the theoretical convergence results and its practical realization. Moreover, we shortly touch related questions for higher-order DAEs. We discuss several practical aspects of higher-order differential–algebraic operators and the associated equations which may be important for the application of collocation methods.
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| 37. |
- Hanke, Michael, et al.
(författare)
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An immersed finite element method and its convergence for elliptic interface problems with discontinuous coefficients and singular sources
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This paper is concerned with the analysis of an immersed ginite element method for two dimensional elliptic interface problems. The main idea of the method is to use specifically designed macro elements in the vicinity of the interface, such that the jump conditions are well approximated. In general, the resulting immersed finite element space is non-conforming. It is shown that the presented method is second order accurate in L² norm. The provided numerical results agree with the theoretical estimates.
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| 38. |
- Hanke, Michael, et al.
(författare)
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Analytical And Numerical Approximation of Effective Diffusivities in The Cytoplasm of Biological Cells
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplsma has a very complex geometric structure which cannot be handled by standard discretization techniques. In the present paper we propose a homogenization technique for computing effective diffusion constants. This is accomplished by using a two-step strategy. The first step consists of an analytic homogenization from the smallest to an intermediate scale. The homogenization error is estimated by comparing the analytic diffusion constant with a numerical estimate obtained by using real cell geometries. The second step consists of a random homogenization. Since no analytical solution is known to this homogenization problem, a numerical approximation algorithm is proposed. Although rather expensive this algorithm provides a reasonable estimate of the homogenized diffusion constant.
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| 39. |
- Hanke, Michael
(författare)
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Benchmarking Femlab 3.0a: Laminar Flows in 2D
- 2004
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Recently, version 3.0a of the software package FEMLAB for solving multiphysics partialdifferential equations was released. In the present project we compared its performance with the previous release 2.3 and the package Fluent 6.1 in stationary laminar flow benchmarkproblems in two and three dimensions. It turns out that the new version is an essential improvement over the old version. It is much faster than Fluent in 2D.
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| 40. |
- Hanke, Michael
(författare)
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Benchmarking Femlab 3.1i: Solid Structural Mechanics
- 2005
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The software package FEMLAB is an environment for modelling and solving multiphysics applications which are described in terms of partial differential differential equations. In this project we tested the performance of the structural mechanics toolbox version 3.1. This version of the toolbox represents a considerable enhancement over previous releases with respect to modelling capabilities. We compare the performance of version 3.1 to that of the older version 2.3 and a state-of-the-art finite element package for solving structural mechanics problems, namely, ANSYS 9.0.
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| 41. |
- Hanke, Michael, et al.
(författare)
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Consistent initialization for nonlinear index-2 differential-algebraic equation : large sparse systems in MATLAB
- 2003
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Ingår i: Numerical Algorithms. - 1017-1398 .- 1572-9265. ; 32:1, s. 67-85
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Tidskriftsartikel (refereegranskat)abstract
- An important component of any initial-value solver for higher-index differential-algebraic equations consists in the computation of consistent initial values. In a recent paper [5], an algorithm is proposed which is applicable to a very general class of index-2 systems. Unfortunately, the computational expense is rather high. We present a modification of this approach, which gives rise to a MATLAB implementation capable of handling systems of moderate dimension (several thousands of unknowns). The algorithm is illustrated by examples.
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| 42. |
- Hanke, Michael, et al.
(författare)
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Convergence analysis of least-squares collocation methods for nonlinear higher-index differential–algebraic equations
- 2021
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Ingår i: Journal of Computational and Applied Mathematics. - : Elsevier BV. - 0377-0427 .- 1879-1778. ; 387
-
Tidskriftsartikel (refereegranskat)abstract
- We approach a direct numerical treatment of nonlinear higher-index differential–algebraic equations by means of overdetermined polynomial least-squares collocation. The procedure is not much more computationally expensive than standard collocation methods for regular ordinary differential equations and the numerical experiments show promising results. Nevertheless, the theoretical basic concept turns out to be considerably challenging. So far, quite recently, convergence proofs have been published for linear problems. In the present paper we come up with a first basic qualitative convergence result for nonlinear problems.
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| 43. |
- Hanke, M., et al.
(författare)
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Football championships and jersey sponsors' stock prices: an empirical investigation
- 2013
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Ingår i: European Journal of Finance. - : Informa UK Limited. - 1351-847X .- 1466-4364. ; 19:3, s. 228-241
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Tidskriftsartikel (refereegranskat)abstract
- Corporate sports sponsorship is an important part of many companies' corporate communication strategy. In this paper, we take the example of major football tournaments to show that sponsorship indeed affects the sponsor's (stock) market value. We find a statistically significant impact of football results (at an individual match level) of the seven most important football nations at European and World Championships on the stock prices of jersey sponsors. In general, the more important a match and the less expected its result, the higher its impact. In addition, we find a form of mere-exposure' effect which is difficult to reconcile with the efficient markets hypothesis.
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| 44. |
- Hanke, Michael, et al.
(författare)
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Least-Squares Collocation for Higher-Index Linear Differential-Algebraic Equations : Estimating the Instability Threshold
- 2019
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Ingår i: Mathematics of Computation. - : American Mathematical Society (AMS). - 0025-5718 .- 1088-6842. ; 88:318, s. 1647-1683
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Tidskriftsartikel (refereegranskat)abstract
- Differential-algebraic equations with higher-index give rise to essentially ill-posed problems. The overdetermined least-squares collocation for differential-algebraic equations which has been proposed recently is not much more computationally expensive than standard collocation methods for ordinary differential equations. This approach has displayed impressive convergence properties in numerical experiments, however, theoretically, till now convergence could be established merely for regular linear differential-algebraic equations with constant coefficients. We present now an estimate of the instability threshold which serves as the basic key for proving convergence for general regular linear differential-algebraic equations.
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| 45. |
- Hanke, Michael, et al.
(författare)
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Least-Squares Collocation for Higher-Index Linear Differential-Algebraic Equations: Estimating the Instability Threshold
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Abstract: Differential-algebraic equations with higher index give rise to essentially ill-posed problems. The least-squares collocation by discretizing the pre-image space is not much more computationally expensive than standard collocation methods used in the numerical solution of ordinary differential equations and index-1 differential-algebraic equations. This approach has displayed excellent convergence properties in numerical experiments, however, theoretically, till now convergence could be established merely for regular linear differential-algebraic equations with constant coefficients. We present now an estimate of the instability threshold which serves as the basic key for proving convergence for general regular linear DAEs.
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| 46. |
- Hanke, Michael, et al.
(författare)
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Least-squares collocation for linear higher-index differential–algebraic equations
- 2017
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Ingår i: Journal of Computational and Applied Mathematics. - : Elsevier. - 0377-0427 .- 1879-1778. ; 317, s. 403-431
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Tidskriftsartikel (refereegranskat)abstract
- Differential–algebraic equations with higher index give rise to essentially ill-posed problems. Therefore, their numerical approximation requires special care. In the present paper, we state the notion of ill-posedness for linear differential–algebraic equations more precisely. Based on this property, we construct a regularization procedure using a least-squares collocation approach by discretizing the pre-image space. Numerical experiments show that the resulting method has excellent convergence properties and is not much more computationally expensive than standard collocation methods used in the numerical solution of ordinary differential equations or index-1 differential–algebraic equations. Convergence is shown for a limited class of linear higher-index differential–algebraic equations.
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| 47. |
- Hanke, Michael
(författare)
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On a variable step size modification of Hines' method in computational neuroscience
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- For simulating large networks of neurons Hines proposed a method which usesextensively the structure of the arising systems of ordinary differentialequations in order to obtain an efficient implementation. The original methodrequires constant step sizes and produces the solution on a staggered grid. Inthe present paper a one-step modification of this method is introduced andanalyzed with respect to their stability properties. The new method allows forstep size control. Local error estimators are constructed. The method has beenimplemented in matlab and tested using simple Hodgkin-Huxley type models.Comparisons with standard state-of-the-art solvers are provided.
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| 48. |
- Hanke, Michael
(författare)
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On the sensitivity of implementations of a least-squares collocation method for linear higher-index differential-algebraic equations
- 2022
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Ingår i: Numerical Algorithms. - : Springer Nature. - 1017-1398 .- 1572-9265. ; 91:4, s. 1721-1754
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Tidskriftsartikel (refereegranskat)abstract
- The present paper continues our investigation of an implementation of a least-squares collocation method for higher-index differential-algebraic equations. In earlier papers, we were able to substantiate the choice of basis functions and collocation points for a robust implementation as well as algorithms for the solution of the discrete system. The present paper is devoted to an analytic estimation of condition numbers for different components of an implementation. We present error estimations, which show the sources for the different errors.
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| 49. |
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| 50. |
- Hanke, Michael, et al.
(författare)
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Simulated annealing for the optimization of batch distillation processes
- 2000
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Ingår i: Computers and Chemical Engineering. - 0098-1354 .- 1873-4375. ; 24:1, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- Batch distillation processes are widely used in the chemical industry. In this work, we consider the optimization of such processes by simulated annealing. Although this method is stochastically in nature, it has two well-known advantages: it can be readily connected to highly sophisticated simulation codes and it converges towards a global optimum. According to the characteristics of batch distillation operation we propose to use a two-step computation approach. A feasible strategy (admissible control) will be searched for in the first step and it will be optimized in the second step. The approach has been applied to a model of a pilot batch distillation plant. These results show the potential of the method for developing optimal operation strategies for batch chemical processes;
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