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  • Fange, David, et al. (författare)
  • Stochastic reaction-diffusion kinetics in the microscopic limit
  • 2010
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 107:46, s. 19820-19825
  • Tidskriftsartikel (refereegranskat)abstract
    • Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system.  
  • Genkin, Michael, et al. (författare)
  • Description of resonance decay by Lindblad operators
  • 2008
  • Ingår i: Journal of Physics A: Mathematical and Theoretical. - 1751-8113. ; 41:42, s. 425303
  • Tidskriftsartikel (refereegranskat)abstract
    • Using an analytical model potential which contains resonant and bound states, we show that the decay of the resonances can be simulated by Lindblad operators. For that purpose, the unitary time evolution of an initial Gaussian wave packet in the model potential is compared with the non-unitary time evolution, obtained by solving the Lindblad equation, of the same wave packet in a potential which coincides with the model potential in the region of interest but does not contain resonances. In the latter case, dissipative effects are accounted for by Lindblad operators which lead to phenomenological friction and diffusion constants in the equations of motion. We suggest how those constants can be determined in a non-heuristic way, being directly connected to the width of the resonance in the model potential which we calculate using the complex rotation method.
  • Huang, J., et al. (författare)
  • Growth of SiC thin films on (100) and (111) silicon by pulsed laser deposition combined with a vacuum annealing process
  • 1999
  • Ingår i: Materials Research Society Symposium - Proceedings. - San Francisco, CA, USA. ; s. 207-212
  • Konferensbidrag (refereegranskat)abstract
    • Crystalline 3C-SiC thin films were successfully grown on (100) and (111) Si substrates by using ArF pulsed laser ablation from a SiC ceramic target combined with a vacuum annealing process. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) were employed to study the effect of annealing on the structure of thin films deposited at 800°C. It was demonstrated that vacuum annealing could transform the amorphous SiC films into crystalline phase and that the crystallinity was strongly dependent on the annealing temperature. For the samples deposited on (100) and (111) Si, the optimum annealing temperatures were 980 and 920°C, respectively. Scanning electron microscope (SEM) micrographs exhibited different characteristic microstructure for the (100) and (111) Si cases, similar to that observed for the carbonization layer initially formed in chemical vapor deposition of SiC films on Si. This also showed the presence of the epitaxial relationship of 3C-SiC[100]//Si[100] and 3C-SiC[111]//Si[111] in the direction of growth.
  • Jung, Daniel, 1984-, et al. (författare)
  • Residual selection for fault detection and isolation using convex optimization
  • 2018
  • Ingår i: Automatica. - Pergamon Press. - 0005-1098. ; 97, s. 143-149
  • Tidskriftsartikel (refereegranskat)abstract
    • In model-based diagnosis there are often more candidate residual generators than what is needed and residual selection is therefore an important step in the design of model-based diagnosis systems. The availability of computer-aided tools for automatic generation of residual generators have made it easier to generate a large set of candidate residual generators for fault detection and isolation. Fault detection performance varies significantly between different candidates due to the impact of model uncertainties and measurement noise. Thus, to achieve satisfactory fault detection and isolation performance, these factors must be taken into consideration when formulating the residual selection problem. Here, a convex optimization problem is formulated as a residual selection approach, utilizing both structural information about the different residuals and training data from different fault scenarios. The optimal solution corresponds to a minimal set of residual generators with guaranteed performance. Measurement data and residual generators from an internal combustion engine test-bed is used as a case study to illustrate the usefulness of the proposed method.
  • Jung, Hannes (författare)
  • Heavy quark production at hera in K-T factorization supplemented with CCFM evolution
  • 2002
  • Ingår i: Photon 2001. - World Scientific. - 9789812380531 ; s. 122-127
  • Konferensbidrag (refereegranskat)abstract
    • The application of k(t) - factorization, supplemented with the CCFM small-x evolution equation, to heavy quark production is discussed. Differential cross sections of b (b) over bar production and also inelastic J/psi production as measured at HERA are compared to the hadron level CCFM Monte Carlo generator CASCADE, using the unintegrated gluon density obtained within the CCFM evolution approach from a fit to HERA F-2 data.
  • Keuper, Frida, et al. (författare)
  • A frozen feast : thawing permafrost increases plant-available nitrogen in subarctic peatlands
  • 2012
  • Ingår i: Global Change Biology. - 1354-1013. ; 18:6, s. 1998-2007
  • Tidskriftsartikel (refereegranskat)abstract
    • Many of the world's northern peatlands are underlain by rapidly thawing permafrost. Because plant production in these peatlands is often nitrogen (N)-limited, a release of N stored in permafrost may stimulate net primary production or change species composition if it is plant-available. In this study, we aimed to quantify plant-available N in thawing permafrost soils of subarctic peatlands. We compared plant-available N-pools and -fluxes in near-surface permafrost (010cm below the thawfront) to those taken from a current rooting zone layer (515cm depth) across five representative peatlands in subarctic Sweden. A range of complementary methods was used: extractions of inorganic and organic N, inorganic and organic N-release measurements at 0.5 and 11 degrees C (over 120days, relevant to different thaw-development scenarios) and a bioassay with Poa alpina test plants. All extraction methods, across all peatlands, consistently showed up to seven times more plant-available N in near-surface permafrost soil compared to the current rooting zone layer. These results were supported by the bioassay experiment, with an eightfold larger plant N-uptake from permafrost soil than from other N-sources such as current rooting zone soil or fresh litter substrates. Moreover, net mineralization rates were much higher in permafrost soils compared to soils from the current rooting zone layer (273mgNm-2 and 1348mgNm-2 per growing season for near-surface permafrost at 0.5 degrees C and 11 degrees C respectively, compared to -30mgNm-2 for current rooting zone soil at 11 degrees C). Hence, our results demonstrate that near-surface permafrost soil of subarctic peatlands can release a biologically relevant amount of plant available nitrogen, both directly upon thawing as well as over the course of a growing season through continued microbial mineralization of organically bound N. Given the nitrogen-limited nature of northern peatlands, this release may have impacts on both plant productivity and species composition.
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